Equivalence class DNA_2.0_10786.8 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3O1M|1|B+ 3O1M|1|C (rep) | DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(ME6)P*AP*CP*CP*GP*T)-3'), DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.75 | 2010-11-17 | ||||
| 2 | 3MR2|1|T+ 3MR2|1|P | DNA (5'-D(*T*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'), DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3') | Human DNA polymerase eta in complex with normal DNA and incoming nucleotide (Nrm) | X-ray diffraction | 1.83 | 2010-06-30 | ||||
| 3 | 3O1P|1|B+ 3O1P|1|C | DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(EDA)P*AP*CP*CP*GP*T)-3'), DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.51 | 2010-11-17 | ||||
| 4 | 3BKZ|1|B+ 3BKZ|1|C | DNA (5'-D(*DTP*DAP*DGP*DGP*DTP*DAP*DAP*DCP*DAP*DTP*DCP*DGP*DT)-3'), DNA (5'-D(*DAP*DAP*DCP*DGP*DAP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3') | X-ray structure of E coli AlkB crosslinked to dsDNA in the active site | X-ray diffraction | 1.65 | 2008-04-22 | ||||
| 5 | 3O1T|1|C+ 3O1T|1|B | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDU)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.48 | 2010-11-17 | ||||
| 6 | 3BIE|1|C+ 3BIE|1|B | DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DTP*DTP*DAP*DCP*DCP*DT)-3'), DNA (5'-D(P*DAP*DGP*DGP*DTP*DAP*DAP*(MA7)P*DAP*DCP*DCP*DGP*DT)-3') | X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG | X-ray diffraction | 1.68 | 2008-04-22 | ||||
| 7 | 3I0W|1|B+ 3I0W|1|C | 5'-D(*AP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*A)-3' | Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing cytosine opposite to 8-oxoG | X-ray diffraction | 1.73 | 2009-09-29 | ||||
| 8 | 3I0X|1|C+ 3I0X|1|D | 5'-D(*AP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*AP*TP*GP*GP*A)-3' | Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing adenine opposite to 8-oxoG | X-ray diffraction | 1.8 | 2009-09-29 | ||||
| 9 | 1SXQ|1|C+ 1SXQ|1|E | 5'-D(*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*AP*CP*TP*TP*TP*TP*TP*T)-3' | BGT in complex with a 13mer DNA containing a central C:G base pair and UDP | X-ray diffraction | 1.8 | 2004-06-22 | ||||
| 10 | 1M5R|1|C+ 1M5R|1|E | 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3', 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3' | Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex | X-ray diffraction | 1.8 | 2002-12-11 | ||||
| 11 | 1SXQ|1|D+ 1SXQ|1|F | 5'-D(*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*AP*CP*TP*TP*TP*TP*TP*T)-3' | BGT in complex with a 13mer DNA containing a central C:G base pair and UDP | X-ray diffraction | 1.8 | 2004-06-22 | ||||
| 12 | 1M5R|1|D+ 1M5R|1|F | 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3', 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3' | Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex | X-ray diffraction | 1.8 | 2002-12-11 | ||||
| 13 | 3O1U|1|C+ 3O1U|1|B | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDV)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.54 | 2010-11-17 | ||||
| 14 | 2HHW|1|C+ 2HHW|1|B | 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3' | ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation | X-ray diffraction | 1.88 | 2006-12-12 | ||||
| 15 | 2HHW|1|F+ 2HHW|1|E | 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3' | ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation | X-ray diffraction | 1.88 | 2006-12-12 | ||||
| 16 | 3O1O|1|B+ 3O1O|1|C | DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(MFT)P*AP*CP*CP*GP*T)-3'), DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.92 | 2010-11-17 | ||||
| 17 | 3O1S|1|C+ 3O1S|1|B | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDQ)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.58 | 2010-11-17 | ||||
| 18 | 3H8R|1|B+ 3H8R|1|C | 5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(6MA)P*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3' | synthetic construct | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-ray diffraction | 1.77 | 2010-03-31 | |||
| 19 | 3O1R|1|C+ 3O1R|1|B | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDK)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.77 | 2010-11-17 | ||||
| 20 | 2HVI|1|C+ 2HVI|1|B | 5'-D(*C*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3' | ddCTP:G pair in the polymerase active site (0 position) | X-ray diffraction | 1.98 | 2006-12-12 | ||||
| 21 | 2HVI|1|F+ 2HVI|1|E | 5'-D(*C*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3' | ddCTP:G pair in the polymerase active site (0 position) | X-ray diffraction | 1.98 | 2006-12-12 | ||||
| 22 | 3BTX|1|B+ 3BTX|1|C | DNA (5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*TP*GP*CP*G)-3'), DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DCP*DA)-3') | X-ray structure of human ABH2 bound to dsDNA through active site cross-linking | X-ray diffraction | 2 | 2008-04-22 | ||||
| 23 | 2UYC|1|C+ 2UYC|1|D | 5'-D(*TP*GP*GP*AP*TP*GP*5CMP*GP*CP*TP *GP*AP*C)-3', 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP *CP*C)-3' | synthetic construct | HhaI DNA methyltransferase R163N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH | X-ray diffraction | 2 | 2008-05-27 | |||
| 24 | 3OHA|1|T+ 3OHA|1|P | 5'-D(P*TP*(8OG)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3', 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3' | Yeast DNA polymerase eta inserting dCTP opposite an 8oxoG lesion | X-ray diffraction | 2 | 2010-12-22 | ||||
| 25 | 3L2C|1|B+ 3L2C|1|C | FOXO consensus binding sequence, plus strand, FOXO consensus binding sequence, minus strand | Crystal Structure of the DNA Binding Domain of FOXO4 Bound to DNA | X-ray diffraction | 1.868 | 2009-12-29 | ||||
| 26 | 3O1V|1|C+ 3O1V|1|B | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDJ)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.9 | 2010-11-17 | ||||
| 27 | 3H8X|1|B+ 3H8X|1|C | 5'-D(*CP*TP*GP*TP*(ME6)P*TP*(2YR)P*AP*TP*TP*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*AP*AP*TP*AP*AP*GP*AP*CP*A)-3' | synthetic construct | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-ray diffraction | 1.95 | 2010-03-31 | |||
| 28 | 2ZO1|1|D+ 2ZO1|1|E | DNA (5'-D(*DTP*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3'), DNA (5'-D(*DGP*DTP*DCP*DAP*DGP*(5CM)P*DGP*DCP*DAP*DAP*DTP*DGP*DG)-3') | Mouse NP95 SRA domain DNA specific complex 2 | X-ray diffraction | 1.96 | 2008-09-09 | ||||
| 29 | 3QZ8|1|P | 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*AP*GP*G)-3' | TT-4 ternary complex of Dpo4 | X-ray diffraction | 1.999 | 2011-04-06 | ||||
| 30 | 3H8O|1|B+ 3H8O|1|C | 5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(MA7)P*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3' | synthetic construct | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-ray diffraction | 2 | 2010-03-31 | |||
| 31 | 1PUY|1|A | 5'-D(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)-3' | 1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker | X-ray diffraction | 1.5 | 2003-10-14 | ||||
| 32 | 1PUY|1|B | 5'-D(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)-3' | 1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker | X-ray diffraction | 1.5 | 2003-10-14 | ||||
| 33 | 3BI3|1|B+ 3BI3|1|C | DNA (5'-D(*TP*AP*GP*GP*TP*AP*AP*(MA7)P*AP*(2YR)P*CP*GP*T)-3'), DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3') | X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors | X-ray diffraction | 1.9 | 2008-04-22 | ||||
| 34 | 3E6C|1|A+ 3E6C|1|B | DNA (5'-D(P*DGP*DGP*DCP*DAP*DTP*DGP*DTP*DTP*DAP*DAP*DTP*DGP*DC)-3'), DNA (5'-D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DGP*DCP*DC)-3') | CprK OCPA DNA Complex | X-ray diffraction | 1.8 | 2008-09-30 | ||||
| 35 | 4BDP|1|T+ 4BDP|1|P | DNA (5'-D(*TP*AP*TP*TP*GP*CP*AP*TP*GP*AP*TP*GP*C)-3'), DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3') | CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES | X-ray diffraction | 1.8 | 1999-01-13 | ||||
| 36 | 1YO5|1|A+ 1YO5|1|B | Enhancer site of Prostate Specific Antigen Promoter Region | Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site | X-ray diffraction | 2 | 2005-05-17 | ||||
| 37 | 1Y8Z|1|C+ 1Y8Z|1|D | 5'-D(*GP*AP*TP*AP*CP*TP*(5HU)P*AP*GP*AP*TP*AP*G)-3', 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*G)-3' | alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a HMU base at 1.9 A resolution | X-ray diffraction | 1.9 | 2005-08-30 | ||||
| 38 | 2OXV|1|C | DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | Structure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site. | X-ray diffraction | 1.95 | 2007-10-23 | ||||
| 39 | 1GD2|1|A+ 1GD2|1|B | DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3') | CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA | X-ray diffraction | 2 | 2000-10-02 | ||||
| 40 | 1GD2|1|C+ 1GD2|1|D | DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3') | CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA | X-ray diffraction | 2 | 2000-10-02 | ||||
| 41 | 1WTE|1|X+ 1WTE|1|Y | 5'-D(*AP*CP*CP*GP*GP*GP*CP*CP*CP*TP*GP*CP*C)-3', 5'-D(*GP*GP*CP*AP*GP*GP*GP*CP*CP*CP*GP*GP*T)-3' | Crystal structure of type II restrcition endonuclease, EcoO109I complexed with cognate DNA | X-ray diffraction | 1.9 | 2004-12-14 | ||||
| 42 | 3QZ7|1|P | 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*G)-3' | T-3 ternary complex of Dpo4 | X-ray diffraction | 1.998 | 2011-04-06 | ||||
| 43 | 3GV5|1|F+ 3GV5|1|E | 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3', 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3' | Human DNA polymerase iota in complex with T template DNA and incoming ddADP | X-ray diffraction | 2 | 2009-06-02 | ||||
| 44 | 3GV5|1|T+ 3GV5|1|P | 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3', 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3' | Human DNA polymerase iota in complex with T template DNA and incoming ddADP | X-ray diffraction | 2 | 2009-06-02 | ||||
| 45 | 3PVV|1|E | DNA (5'-D(*CP*GP*TP*TP*GP*TP*CP*CP*AP*CP*AP*AP*C)-3') | Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA | X-ray diffraction | 2 | 2011-05-25 | ||||
| 46 | 3PVV|1|D | DNA (5'-D(*GP*TP*TP*GP*TP*GP*GP*AP*CP*AP*AP*CP*G)-3') | Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA | X-ray diffraction | 2 | 2011-05-25 | ||||
| 47 | 3PVV|1|F | DNA (5'-D(*GP*TP*TP*GP*TP*GP*GP*AP*CP*AP*AP*CP*G)-3') | Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA | X-ray diffraction | 2 | 2011-05-25 | ||||
| 48 | 3PVV|1|C | DNA (5'-D(*CP*GP*TP*TP*GP*TP*CP*CP*AP*CP*AP*AP*C)-3') | Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA | X-ray diffraction | 2 | 2011-05-25 | ||||
| 49 | 1K3X|1|B+ 1K3X|1|C | 5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3', 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' | Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA | X-ray diffraction | 1.25 | 2002-10-04 | ||||
| 50 | 1K3W|1|B+ 1K3W|1|C | 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3', 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' | Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA | X-ray diffraction | 1.42 | 2002-10-04 | ||||
| 51 | 1LLM|1|A+ 1LLM|1|B | 5'-D(*TP*CP*CP*CP*AP*CP*GP*CP*GP*TP*GP*GP*G)-3' | Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA | X-ray diffraction | 1.5 | 2003-09-30 | ||||
| 52 | 1QUM|1|D+ 1QUM|1|C+ 1QUM|1|B | 5'-D(*CP*GP*TP*CP*C)-3', 5'-D(*(3DR)P*CP*GP*AP*CP*GP*A)-3', 5'-D(*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*G)-3' | CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA | X-ray diffraction | 1.55 | 1999-08-31 | ||||
| 53 | 3PVI|1|C+ 3PVI|1|D | DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3') | D34G MUTANT OF PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DNA SHOWS THAT ASP34 IS DIRECTLY INVOLVED IN DNA RECOGNITION AND INDIRECTLY INVOLVED IN CATALYSIS | X-ray diffraction | 1.59 | 1998-10-14 | ||||
| 54 | 1DC1|1|C+ 1DC1|1|W | DNA (5'-D(*T*AP*TP*AP*CP*TP*CP*GP*AP*GP*TP*AP*T)-3') | RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD | X-ray diffraction | 1.7 | 2001-02-21 | ||||
| 55 | 2PVI|1|C+ 2PVI|1|D | DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*(C38)P*TP*GP*GP*TP*C)-3') | PVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DNA | X-ray diffraction | 1.76 | 1999-12-20 | ||||
| 56 | 1EYU|1|C+ 1EYU|1|D | DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3') | HIGH RESOLUTION STRUCTURE OF THE PVUII ENDONCULEASE/COGNATE DNA COMPLEX AT PH 4.6 | X-ray diffraction | 1.78 | 2000-07-21 | ||||
| 57 | 1CL8|1|B | DNA (5'-D(*TP*CP*GP*CP*GP*AP*(PRN)P*TP*TP*CP*GP*CP*G)-3') | A PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAPTTCGCG) COMPLEX WITH DNA BASE ANALOG PURINE (P) | X-ray diffraction | 1.8 | 1999-05-19 | ||||
| 58 | 1A73|1|C+ 1A73|1|E+ 1A73|1|D+ 1A73|1|F | DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3'), DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3') | INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA | X-ray diffraction | 1.8 | 1998-10-14 | ||||
| 59 | 1CKQ|1|B | DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAATTCGCG) COMPLEX | X-ray diffraction | 1.85 | 1999-04-26 | ||||
| 60 | 2C7Q|1|C+ 2C7Q|1|D | 5'-D(*T*GP*GP*(2PR)*GP*GP*(5CM)*GP*CP*TP*GP* AP*C)-3', 5'-D(*T*GP*TP*CP*AP*GP*CP*GP*CP*CP*GP*CP*C)-3' | synthetic construct | HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine outside the recognition sequence (paired with G) and SAH | X-ray diffraction | 1.85 | 2005-12-14 | |||
| 61 | 2C7O|1|C+ 2C7O|1|D | 5'-D(*T*GP*GP*AP*TP*GP*(5CM)*GP*CP*TP*GP*AP *C)-3', 5'-D(*T*GP*TP*CP*AP*(2PR)*CP*GP*CP*AP*TP*CP *C)-3' | synthetic construct | HhaI DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (PCGC:GMGC) and SAH | X-ray diffraction | 1.9 | 2005-12-14 | |||
| 62 | 2HR1|1|D+ 2HR1|1|C | 5'-D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3', 5'-D(*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3' | Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy | X-ray diffraction | 1.96 | 2006-09-19 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
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Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5
#S - ordering by similarity (same as in the heat map).| #S | PDB | Title | Method | Resolution | Length | NAKB_NA_annotation | NAKB_protein_annotation |
|---|---|---|---|---|---|---|---|
| 1 | 1Y8Z|1|C+1Y8Z|1|D | alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a HMU base at 1.9 A resolution | X-RAY DIFFRACTION | 1.9 | 13 | enzyme,transferase | |
| 2 | 2HHW|1|F+2HHW|1|E | ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation | X-RAY DIFFRACTION | 1.88 | 13 | double helix,structure | enzyme,polymerase,transferase |
| 3 | 2HHW|1|C+2HHW|1|B | ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation | X-RAY DIFFRACTION | 1.88 | 13 | double helix,structure | enzyme,polymerase,transferase |
| 4 | 2HVI|1|F+2HVI|1|E | ddCTP:G pair in the polymerase active site (0 position) | X-RAY DIFFRACTION | 1.98 | 13 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 5 | 2HVI|1|C+2HVI|1|B | ddCTP:G pair in the polymerase active site (0 position) | X-RAY DIFFRACTION | 1.98 | 13 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 6 | 3MR2|1|T+3MR2|1|P | Human DNA polymerase eta in complex with normal DNA and incoming nucleotide (Nrm) | X-RAY DIFFRACTION | 1.83 | 13 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 7 | 3BTX|1|B+3BTX|1|C | X-ray structure of human ABH2 bound to dsDNA through active site cross-linking | X-RAY DIFFRACTION | 2 | 13 | enzyme,oxidoreductase | |
| 8 | 3H8R|1|B+3H8R|1|C | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-RAY DIFFRACTION | 1.77 | 13 | enzyme,oxidoreductase | |
| 9 | 3H8O|1|B+3H8O|1|C | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-RAY DIFFRACTION | 2 | 13 | enzyme,oxidoreductase | |
| 10 | 1YO5|1|A+1YO5|1|B | Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site | X-RAY DIFFRACTION | 2 | 13 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 11 | 3PVV|1|D | Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA | X-RAY DIFFRACTION | 2 | 26 | B-form double helix,double helix,structure | DNA replication/repair,regulatory |
| 12 | 3PVV|1|F | Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA | X-RAY DIFFRACTION | 2 | 24 | B-form double helix,double helix,structure | DNA replication/repair,regulatory |
| 13 | 3QZ8|1|P | TT-4 ternary complex of Dpo4 | X-RAY DIFFRACTION | 1.999 | 33 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 14 | 3QZ7|1|P | T-3 ternary complex of Dpo4 | X-RAY DIFFRACTION | 1.998 | 19 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 15 | 3L2C|1|B+3L2C|1|C | Crystal Structure of the DNA Binding Domain of FOXO4 Bound to DNA | X-RAY DIFFRACTION | 1.868 | 13 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 16 | 1GD2|1|C+1GD2|1|D | CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA | X-RAY DIFFRACTION | 2 | 13 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription |
| 17 | 1GD2|1|A+1GD2|1|B | CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA | X-RAY DIFFRACTION | 2 | 13 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription |
| 18 | 3OHA|1|T+3OHA|1|P | Yeast DNA polymerase eta inserting dCTP opposite an 8oxoG lesion | X-RAY DIFFRACTION | 2 | 13 | double helix,structure | enzyme,polymerase,transferase |
| 19 | 1SXQ|1|C+1SXQ|1|E | BGT in complex with a 13mer DNA containing a central C:G base pair and UDP | X-RAY DIFFRACTION | 1.8 | 13 | B-form double helix,double helix,structure | enzyme,transferase |
| 20 | 1SXQ|1|D+1SXQ|1|F | BGT in complex with a 13mer DNA containing a central C:G base pair and UDP | X-RAY DIFFRACTION | 1.8 | 13 | B-form double helix,double helix,structure | enzyme,transferase |
| 21 | 1K3X|1|B+1K3X|1|C | Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA | X-RAY DIFFRACTION | 1.25 | 13 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 22 | 1K3W|1|B+1K3W|1|C | Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA | X-RAY DIFFRACTION | 1.42 | 13 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 23 | 1LLM|1|A+1LLM|1|B | Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA | X-RAY DIFFRACTION | 1.5 | 13 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription |
| 24 | 3PVV|1|E | Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA | X-RAY DIFFRACTION | 2 | 32 | B-form double helix,double helix,structure | DNA replication/repair,regulatory |
| 25 | 3PVV|1|C | Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA | X-RAY DIFFRACTION | 2 | 23 | B-form double helix,double helix,structure | DNA replication/repair,regulatory |
| 26 | 3E6C|1|A+3E6C|1|B | CprK OCPA DNA Complex | X-RAY DIFFRACTION | 1.8 | 13 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 27 | 1EYU|1|C+1EYU|1|D | HIGH RESOLUTION STRUCTURE OF THE PVUII ENDONCULEASE/COGNATE DNA COMPLEX AT PH 4.6 | X-RAY DIFFRACTION | 1.78 | 13 | double helix,structure | enzyme,hydrolase,nuclease |
| 28 | 2PVI|1|C+2PVI|1|D | PVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DNA | X-RAY DIFFRACTION | 1.76 | 13 | double helix,structure | enzyme,hydrolase,nuclease |
| 29 | 3PVI|1|C+3PVI|1|D | D34G MUTANT OF PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DNA SHOWS THAT ASP34 IS DIRECTLY INVOLVED IN DNA RECOGNITION AND INDIRECTLY INVOLVED IN CATALYSIS | X-RAY DIFFRACTION | 1.59 | 13 | double helix,structure | enzyme,hydrolase,nuclease |
| 30 | 1WTE|1|X+1WTE|1|Y | Crystal structure of type II restrcition endonuclease, EcoO109I complexed with cognate DNA | X-RAY DIFFRACTION | 1.9 | 13 | double helix,structure | enzyme,hydrolase,nuclease |
| 31 | 1A73|1|C+1A73|1|E+1A73|1|D+1A73|1|F | INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA | X-RAY DIFFRACTION | 1.8 | 13 | double helix,structure | enzyme,hydrolase,nuclease |
| 32 | 1CKQ|1|B | PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAATTCGCG) COMPLEX | X-RAY DIFFRACTION | 1.85 | 13 | double helix,structure | enzyme,hydrolase,nuclease |
| 33 | 1CL8|1|B | A PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAPTTCGCG) COMPLEX WITH DNA BASE ANALOG PURINE (P) | X-RAY DIFFRACTION | 1.8 | 13 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 34 | 2OXV|1|C | Structure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site. | X-RAY DIFFRACTION | 1.95 | 13 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 35 | 1DC1|1|C+1DC1|1|W | RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD | X-RAY DIFFRACTION | 1.7 | 13 | double helix,structure | enzyme,hydrolase,nuclease |
| 36 | 2ZO1|1|D+2ZO1|1|E | Mouse NP95 SRA domain DNA specific complex 2 | X-RAY DIFFRACTION | 1.96 | 13 | B-form double helix,double helix,structure | enzyme,ligase |
| 37 | 3GV5|1|F+3GV5|1|E | Human DNA polymerase iota in complex with T template DNA and incoming ddADP | X-RAY DIFFRACTION | 2 | 13 | enzyme,polymerase,transferase | |
| 38 | 3GV5|1|T+3GV5|1|P | Human DNA polymerase iota in complex with T template DNA and incoming ddADP | X-RAY DIFFRACTION | 2 | 13 | enzyme,polymerase,transferase | |
| 39 | 3I0W|1|B+3I0W|1|C | Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing cytosine opposite to 8-oxoG | X-RAY DIFFRACTION | 1.73 | 13 | B-form double helix,double helix,structure | enzyme,hydrolase |
| 40 | 3I0X|1|C+3I0X|1|D | Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing adenine opposite to 8-oxoG | X-RAY DIFFRACTION | 1.8 | 13 | B-form double helix,double helix,structure | enzyme,hydrolase |
| 41 | 1QUM|1|D+1QUM|1|C+1QUM|1|B | CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA | X-RAY DIFFRACTION | 1.55 | 13 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 42 | 4BDP|1|T+4BDP|1|P | CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES | X-RAY DIFFRACTION | 1.8 | 13 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 43 | 2UYC|1|C+2UYC|1|D | HhaI DNA methyltransferase R163N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH | X-RAY DIFFRACTION | 2 | 13 | double helix,structure | enzyme,methylase,transferase |
| 44 | 2C7Q|1|C+2C7Q|1|D | HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine outside the recognition sequence (paired with G) and SAH | X-RAY DIFFRACTION | 1.85 | 13 | enzyme,methylase,transferase | |
| 45 | 2C7O|1|C+2C7O|1|D | HhaI DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (PCGC:GMGC) and SAH | X-RAY DIFFRACTION | 1.9 | 13 | B-form double helix,double helix,structure | enzyme,methylase,transferase |
| 46 | 2HR1|1|D+2HR1|1|C | Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy | X-RAY DIFFRACTION | 1.96 | 13 | B-form double helix,double helix,structure | enzyme,methylase,transferase |
| 47 | 1M5R|1|D+1M5R|1|F | Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex | X-RAY DIFFRACTION | 1.8 | 13 | enzyme,transferase | |
| 48 | 1M5R|1|C+1M5R|1|E | Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex | X-RAY DIFFRACTION | 1.8 | 13 | enzyme,transferase | |
| 49 | 3H8X|1|B+3H8X|1|C | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-RAY DIFFRACTION | 1.95 | 13 | enzyme,oxidoreductase | |
| 50 | 3O1O|1|B+3O1O|1|C | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.92 | 13 | enzyme,oxidoreductase | |
| 51 | 3O1M|1|B+3O1M|1|C | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.75 | 13 | enzyme,oxidoreductase | |
| 52 | 3O1P|1|B+3O1P|1|C | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.51 | 13 | enzyme,oxidoreductase | |
| 53 | 3BI3|1|B+3BI3|1|C | X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors | X-RAY DIFFRACTION | 1.9 | 13 | enzyme,oxidoreductase | |
| 54 | 3BIE|1|C+3BIE|1|B | X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG | X-RAY DIFFRACTION | 1.68 | 13 | enzyme,oxidoreductase | |
| 55 | 3O1V|1|C+3O1V|1|B | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.9 | 13 | enzyme,oxidoreductase | |
| 56 | 3O1S|1|C+3O1S|1|B | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.58 | 13 | enzyme,oxidoreductase | |
| 57 | 3O1U|1|C+3O1U|1|B | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.54 | 13 | enzyme,oxidoreductase | |
| 58 | 3O1R|1|C+3O1R|1|B | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.77 | 13 | enzyme,oxidoreductase | |
| 59 | 3O1T|1|C+3O1T|1|B | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.48 | 13 | enzyme,oxidoreductase | |
| 60 | 3BKZ|1|B+3BKZ|1|C | X-ray structure of E coli AlkB crosslinked to dsDNA in the active site | X-RAY DIFFRACTION | 1.65 | 13 | B-form double helix,double helix,feature,mispair,structure | enzyme,oxidoreductase |
| 61 | 1PUY|1|B | 1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker | X-RAY DIFFRACTION | 1.5 | 13 | B-form double helix,double helix,structure | |
| 62 | 1PUY|1|A | 1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker | X-RAY DIFFRACTION | 1.5 | 13 | B-form double helix,double helix,structure |
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