Equivalence class DNA_4.0_06452.2 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1ENN|1|A+ 1ENN|1|B (rep) | DNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3') | SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE OF D(GCGAATTCG)2 AT ATOMIC RESOLUTION | X-ray diffraction | 0.89 | 2000-05-03 | ||||
| 2 | 1XJY|1|A+ 1XJY|1|B | 5'-D(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3', 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3' | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-ray diffraction | 2 | 2005-03-15 | ||||
| 3 | 3OQG|1|C+ 3OQG|1|D | DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3', DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3' | Restriction endonuclease HPY188I in complex with substrate DNA | X-ray diffraction | 1.75 | 2010-10-20 | ||||
| 4 | 3G00|1|H+ 3G00|1|I | 5'-D(*CP*GP*TP*AP*TP*TP*AP*CP*G)-3', 5'-D(*CP*GP*TP*AP*UP*TP*AP*CP*G)-3' | Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom | X-ray diffraction | 1.74 | 2010-03-09 | ||||
| 5 | 2GB7|1|E+ 2GB7|1|F | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-ray diffraction | 1.7 | 2006-06-20 | ||||
| 6 | 2GB7|1|G+ 2GB7|1|H | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-ray diffraction | 1.7 | 2006-06-20 | ||||
| 7 | 1XJX|1|A+ 1XJX|1|B | 5'-D(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3', 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3' | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-ray diffraction | 1.7 | 2005-03-15 | ||||
| 8 | 3GV8|1|T+ 3GV8|1|P | 5'-D(*AP*TP*GP*GP*GP*TP*CP*CP*T)-3', 5'-D(*AP*GP*GP*AP*CP*CP*C)-3' | Human DNA polymerase iota in complex with T template DNA and incoming dGTP | X-ray diffraction | 2 | 2009-06-02 | ||||
| 9 | 3IMB|1|E+ 3IMB|1|F | 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3', 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 2010-08-11 | ||||
| 10 | 3IMB|1|G+ 3IMB|1|H | 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3', 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 2010-08-11 | ||||
| 11 | 3IMB|1|I+ 3IMB|1|J | 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3', 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 2010-08-11 | ||||
| 12 | 3IMB|1|K+ 3IMB|1|L | 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3', 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 2010-08-11 | ||||
| 13 | 2FQZ|1|E+ 2FQZ|1|F | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-ray diffraction | 2 | 2006-06-20 | ||||
| 14 | 2FQZ|1|G+ 2FQZ|1|H | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-ray diffraction | 2 | 2006-06-20 | ||||
| 15 | 3HQF|1|B+ 3HQF|1|C | 5'-D(*GP*CP*CP*CP*TP*GP*GP*CP*G)-3', 5'-D(*CP*GP*CP*CP*AP*GP*GP*GP*C)-3' | Crystal structure of restriction endonuclease EcoRII N-terminal effector-binding domain in complex with cognate DNA | X-ray diffraction | 2.51 | 2009-09-22 | ||||
| 16 | 2W35|1|F | 5'-D(*AP*TP*GP*CP*GP*AP*CP*IP*GP)-3' | Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair | X-ray diffraction | 2.15 | 2009-01-20 | ||||
| 17 | 3GV7|1|T+ 3GV7|1|P | 5'-D(P*AP*TP*GP*GP*GP*TP*CP*CP*T)-3', 5'-D(*AP*GP*GP*AP*CP*CP*C)-3' | Human DNA polymerase iota in complex with T template DNA and incoming dTTP | X-ray diffraction | 2.2 | 2009-06-02 | ||||
| 18 | 3H4D|1|T+ 3H4D|1|P | 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T), 5'-D(*AP*GP*GP*AP*CP*CP*(DOC)) | Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP | X-ray diffraction | 2.2 | 2009-07-21 | ||||
| 19 | 1RXW|1|C+ 1RXW|1|B | 5'-d(*T*pA*pG*pC*pA*pT*pC*pG*pG)-3', 5'-d(*C*pG*pA*pT*pG*pC*pT*pA)-3' | Crystal structure of A. fulgidus FEN-1 bound to DNA | X-ray diffraction | 2 | 2004-01-27 | ||||
| 20 | 2DPJ|1|T+ 2DPJ|1|P | 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3', 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3' | structure of hPoli with DNA and dTTP | X-ray diffraction | 2.3 | 2006-07-04 | ||||
| 21 | 3H40|1|T+ 3H40|1|P | 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3', 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T)-3' | Binary complex of human DNA polymerase iota with template U/T | X-ray diffraction | 2.3 | 2009-07-21 | ||||
| 22 | 2ALZ|1|T+ 2ALZ|1|P | 5'-D(*TP*GP*GP*GP*GP*TP*CP*CP*T)-3', 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3' | Ternary Complex of hPoli with DNA and dCTP | X-ray diffraction | 2.5 | 2005-10-25 | ||||
| 23 | 2DPI|1|T+ 2DPI|1|P | 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3', 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3' | Ternary complex of hPoli with DNA and dCTP | X-ray diffraction | 2.3 | 2006-07-04 | ||||
| 24 | 3OGD|1|B+ 3OGD|1|C | 5'-D(*GP*CP*AP*GP*TP*CP*AP*TP*G)-3', 5'-D(*CP*AP*(BRU)P*GP*AP*CP*(BRU)P*GP*C)-3' | AlkA Undamaged DNA Complex: Interrogation of a G*:C base pair | X-ray diffraction | 2.8 | 2010-09-15 | ||||
| 25 | 3G4T|1|H+ 3G4T|1|I | 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3', 5'-D(*CP*G*TP*AP*CP*TP*AP*CP*G)-3' | Mth0212 (WT) in complex with a 7bp dsDNA | X-ray diffraction | 2.64 | 2010-03-09 | ||||
| 26 | 3H4B|1|T+ 3H4B|1|P | 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T)-3', 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3' | Ternary complex of human DNA polymerase iota with template U/T and incoming dATP | X-ray diffraction | 2.85 | 2009-07-21 | ||||
| 27 | 3G3C|1|H+ 3G3C|1|I | 5'-D(*CP*GP*TP*AP*CP*TP*AP*CP*G)-3', 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3' | Mth0212 (WT) in complex with a 6bp dsDNA containing a single one nucleotide long 3'-overhang | X-ray diffraction | 3.04 | 2010-03-09 | ||||
| 28 | 208D|1|A+ 208D|1|B | DNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3') | HIGH-RESOLUTION STRUCTURE OF A DNA HELIX FORMING (C.G)*G BASE TRIPLETS | X-ray diffraction | 2.05 | 1995-09-15 | ||||
| 29 | 253D|1|A | DNA (5'-D(*GP*CP*GP*TP*AP*CP*GP*CP*G)-3') | CRYSTAL STRUCTURE OF THE B-DNA NONAMER D(GCGTACGCG) WITH A NOVEL D[G*(G.C)] BASE-TRIPLET INVOLVING THE MINOR GROOVE | X-ray diffraction | 2.2 | 1996-04-15 | ||||
| 30 | 1DN6|1|A+ 1DN6|1|B | DNA (5'-D(*GP*GP*AP*TP*GP*GP*GP*AP*G)-3'), DNA (5'-D(*CP*TP*CP*CP*CP*AP*TP*CP*C)-3') | THE CRYSTAL STRUCTURE OF D(GGATGGGAG). AN ESSENTIAL PART OF THE BINDING SITE FOR TRANSCRIPTION FACTOR IIIA | X-ray diffraction | 3 | 1988-01-16 |
Release history
| Release | 0.19 |
|---|---|
| Date | 2011-05-28 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|
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 | 3IMB|1|K+3IMB|1|L | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 9 | double helix,structure | enzyme,hydrolase,nuclease |
| 2 | 3IMB|1|G+3IMB|1|H | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 9 | double helix,structure | enzyme,hydrolase,nuclease |
| 3 | 3IMB|1|E+3IMB|1|F | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 9 | double helix,structure | enzyme,hydrolase,nuclease |
| 4 | 3IMB|1|I+3IMB|1|J | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 9 | double helix,structure | enzyme,hydrolase,nuclease |
| 5 | 2W35|1|F | Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair | X-RAY DIFFRACTION | 2.15 | 9 | enzyme,hydrolase,nuclease | |
| 6 | 253D|1|A | CRYSTAL STRUCTURE OF THE B-DNA NONAMER D(GCGTACGCG) WITH A NOVEL D[G*(G.C)] BASE-TRIPLET INVOLVING THE MINOR GROOVE | X-RAY DIFFRACTION | 2.2 | 9 | B-form double helix,double helix,structure | |
| 7 | 1RXW|1|C+1RXW|1|B | Crystal structure of A. fulgidus FEN-1 bound to DNA | X-RAY DIFFRACTION | 2 | 9 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease,regulatory,transcription |
| 8 | 3OQG|1|C+3OQG|1|D | Restriction endonuclease HPY188I in complex with substrate DNA | X-RAY DIFFRACTION | 1.75 | 9 | double helix,structure | enzyme,hydrolase,nuclease |
| 9 | 2ALZ|1|T+2ALZ|1|P | Ternary Complex of hPoli with DNA and dCTP | X-RAY DIFFRACTION | 2.5 | 9 | enzyme,polymerase,transferase | |
| 10 | 2DPJ|1|T+2DPJ|1|P | structure of hPoli with DNA and dTTP | X-RAY DIFFRACTION | 2.3 | 9 | enzyme,polymerase,transferase | |
| 11 | 3GV7|1|T+3GV7|1|P | Human DNA polymerase iota in complex with T template DNA and incoming dTTP | X-RAY DIFFRACTION | 2.2 | 9 | double helix,structure | enzyme,polymerase,transferase |
| 12 | 3GV8|1|T+3GV8|1|P | Human DNA polymerase iota in complex with T template DNA and incoming dGTP | X-RAY DIFFRACTION | 2 | 9 | double helix,structure | enzyme,polymerase,transferase |
| 13 | 3H4B|1|T+3H4B|1|P | Ternary complex of human DNA polymerase iota with template U/T and incoming dATP | X-RAY DIFFRACTION | 2.85 | 9 | enzyme,polymerase,transferase | |
| 14 | 3H40|1|T+3H40|1|P | Binary complex of human DNA polymerase iota with template U/T | X-RAY DIFFRACTION | 2.3 | 9 | double helix,structure | enzyme,polymerase,transferase |
| 15 | 3H4D|1|T+3H4D|1|P | Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP | X-RAY DIFFRACTION | 2.2 | 9 | double helix,structure | enzyme,polymerase,transferase |
| 16 | 2DPI|1|T+2DPI|1|P | Ternary complex of hPoli with DNA and dCTP | X-RAY DIFFRACTION | 2.3 | 9 | enzyme,polymerase,transferase | |
| 17 | 1DN6|1|A+1DN6|1|B | THE CRYSTAL STRUCTURE OF D(GGATGGGAG). AN ESSENTIAL PART OF THE BINDING SITE FOR TRANSCRIPTION FACTOR IIIA | X-RAY DIFFRACTION | 3 | 9 | double helix,structure | |
| 18 | 1XJY|1|A+1XJY|1|B | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-RAY DIFFRACTION | 2 | 9 | A-form double helix,double helix,structure | |
| 19 | 3HQF|1|B+3HQF|1|C | Crystal structure of restriction endonuclease EcoRII N-terminal effector-binding domain in complex with cognate DNA | X-RAY DIFFRACTION | 2.51 | 9 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 20 | 3G3C|1|H+3G3C|1|I | Mth0212 (WT) in complex with a 6bp dsDNA containing a single one nucleotide long 3'-overhang | X-RAY DIFFRACTION | 3.04 | 9 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 21 | 3G4T|1|H+3G4T|1|I | Mth0212 (WT) in complex with a 7bp dsDNA | X-RAY DIFFRACTION | 2.64 | 9 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 22 | 3G00|1|H+3G00|1|I | Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom | X-RAY DIFFRACTION | 1.74 | 9 | B-form double helix,double helix,feature,mispair,structure | enzyme,hydrolase,nuclease |
| 23 | 1XJX|1|A+1XJX|1|B | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-RAY DIFFRACTION | 1.7 | 9 | A-form double helix,double helix,structure | |
| 24 | 3OGD|1|B+3OGD|1|C | AlkA Undamaged DNA Complex: Interrogation of a G*:C base pair | X-RAY DIFFRACTION | 2.8 | 9 | B-form double helix,double helix,structure | enzyme,hydrolase |
| 25 | 1ENN|1|A+1ENN|1|B | SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE OF D(GCGAATTCG)2 AT ATOMIC RESOLUTION | X-RAY DIFFRACTION | 0.89 | 9 | B-form double helix,double helix,structure | |
| 26 | 208D|1|A+208D|1|B | HIGH-RESOLUTION STRUCTURE OF A DNA HELIX FORMING (C.G)*G BASE TRIPLETS | X-RAY DIFFRACTION | 2.05 | 9 | B-form double helix,double helix,structure | |
| 27 | 2FQZ|1|G+2FQZ|1|H | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-RAY DIFFRACTION | 2 | 9 | B-form double helix,double helix,structure | enzyme,hydrolase |
| 28 | 2GB7|1|G+2GB7|1|H | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-RAY DIFFRACTION | 1.7 | 9 | B-form double helix,double helix,structure | enzyme,hydrolase |
| 29 | 2GB7|1|E+2GB7|1|F | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-RAY DIFFRACTION | 1.7 | 9 | B-form double helix,double helix,structure | enzyme,hydrolase |
| 30 | 2FQZ|1|E+2FQZ|1|F | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-RAY DIFFRACTION | 2 | 9 | B-form double helix,double helix,structure | enzyme,hydrolase |
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