#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
1476D|1|A+ 476D|1|B (rep)5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'CALCIUM FORM OF B-DNA UNDECAMER GCGAATTCGCGX-ray diffraction1.31999-07-19
23GOX|1|C+ 3GOX|1|D5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3', 5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3'Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I in the absence of EDTAX-ray diffraction1.52009-04-28
33MR3|1|T+ 3MR3|1|PDNA (5'-D(*CP*AP*(TTD)P*AP*TP*GP*AP*CP*GP*CP*T)-3'), DNA (5'-D(*CP*AP*GP*CP*GP*TP*CP*AP*T)-3')Human DNA polymerase eta - DNA ternary complex with the 3'T of a CPD in the active site (TT1)X-ray diffraction1.752010-06-30
43FC3|1|D5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3', 5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3'Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99IX-ray diffraction1.752009-03-31
51TEZ|1|I+ 1TEZ|1|J5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3', 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANSX-ray diffraction1.82004-12-14
61TEZ|1|K+ 1TEZ|1|L5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3', 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANSX-ray diffraction1.82004-12-14
73PNC|1|C+ 3PNC|1|B+ 3PNC|1|D5'-D(*CP*AP*GP*TP*AP*G)-3', 5'-D(*CP*GP*GP*CP*CP*TP*TP*AP*CP*TP*G)-3', 5'-D(*GP*CP*CP*G)-3'Ternary crystal structure of a polymerase lambda variant with a GT mispair at the primer terminus and sodium at catalytic metal siteX-ray diffraction22011-02-02
81ORN|1|B+ 1ORN|1|C5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3', 5'-D(*T*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*T)-3'Structure of a Trapped Endonuclease III-DNA Covalent Intermediate: Estranged-Guanine ComplexX-ray diffraction1.72003-07-15
92PFN|1|T+ 2PFN|1|P+ 2PFN|1|DDownstream Primer, Primer, TemplateNa in the active site of DNA Polymerase lambdaX-ray diffraction1.92007-05-15
102PFO|1|T+ 2PFO|1|P+ 2PFO|1|DDownstream Primer, Primer, TemplateDNA Polymerase lambda in complex with DNA and dUPNPPX-ray diffraction22007-05-15
111XSN|1|T+ 1XSN|1|P+ 1XSN|1|D5'-D(P*GP*CP*CP*G)-3', 5'-D(*CP*AP*GP*TP*AP*(2DT))-3', 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddTTPX-ray diffraction1.952005-01-18
123Q8P|1|TDNA (5'-D(*TP*CP*AP*(8OG)P*GP*GP*GP*TP*CP*CP*T)-3')synthetic constructHuman DNA polymerase iota incorporating dCTP opposite 8-oxo-guanineX-ray diffraction1.952011-02-23
133MQY|1|D+ 3MQY|1|F+ 3MQY|1|C+ 3MQY|1|EDNA (5'-D(P*CP*CP*GP*GP*TP*GP*GP*AP*CP*TP*C)-3'), DNA (5'-D(*GP*AP*GP*TP*CP*CP*A)-3')SgrAI with cleaved DNA and Magnesium boundX-ray diffraction22010-11-24
143MDC|1|T+ 3MDC|1|P+ 3MDC|1|DDNA (5'-D(P*GP*CP*CP*G)-3'), DNA (5'-D(*CP*AP*GP*TP*AP*C)-3'), DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3')DNA polymerase lambda in complex with dFdCTPX-ray diffraction1.9992010-04-28
151AAY|1|B+ 1AAY|1|CDNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3'), DNA (5'-D(*TP*AP*CP*GP*CP*CP*CP*AP*CP*GP*C)-3')ZIF268 ZINC FINGER-DNA COMPLEXX-ray diffraction1.61997-04-21
161A1H|1|B+ 1A1H|1|CDNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*AP*C)-3'), DNA (5'-D(*TP*GP*TP*GP*CP*CP*CP*AP*CP*GP*C)-3')QGSR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCAC SITE)X-ray diffraction1.61998-06-10
171A1I|1|B+ 1A1I|1|CDNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*AP*C)-3'), DNA (5'-D(*TP*GP*TP*GP*CP*CP*CP*AP*CP*GP*C)-3')RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCAC SITE)X-ray diffraction1.61998-06-17
181EON|1|C+ 1EON|1|DDNA (5'-D(*AP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3'), DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3')ECORV BOUND TO 3'-S-PHOSPHOROTHIOLATE DNA AND CA2+X-ray diffraction1.62000-04-04
191JK2|1|B+ 1JK2|1|C5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*TP*G)-3', 5'-D(*TP*CP*AP*GP*CP*CP*CP*AP*CP*GP*C)-3'Zif268 D20A mutant bound to the GCT DNA siteX-ray diffraction1.652001-10-19
201SUZ|1|C+ 1SUZ|1|D5'-D(*C*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'The structure of K92A EcoRV bound to cognate DNA and Mg2+X-ray diffraction1.82004-04-06
211E3O|1|A+ 1E3O|1|B5'-D(*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*A)-3', 5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*T)-3'Homo sapiensCrystal structure of Oct-1 POU dimer bound to MOREX-ray diffraction1.92001-11-10
221A1K|1|B+ 1A1K|1|CDNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3'), DNA (5'-D(*TP*GP*GP*TP*CP*CP*CP*AP*CP*GP*C)-3')RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GACC SITE)X-ray diffraction1.91998-06-10
231JK1|1|B+ 1JK1|1|C5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*G)-3', 5'-D(*TP*CP*CP*GP*CP*CP*CP*AP*CP*GP*C)-3'Zif268 D20A Mutant Bound to WT DNA SiteX-ray diffraction1.92001-10-19
241A1G|1|B+ 1A1G|1|CDNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3'), DNA (5'-D(*TP*AP*CP*GP*CP*CP*CP*AP*CP*GP*C)-3')DSNR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCGT SITE)X-ray diffraction1.91998-06-10
251SSP|1|B+ 1SSP|1|A5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3', 5'-D(*CP*TP*GP*TP*(D1P)P*AP*TP*CP*TP*T)-3'WILD-TYPE URACIL-DNA GLYCOSYLASE BOUND TO URACIL-CONTAINING DNAX-ray diffraction1.91999-05-06
261B94|1|C+ 1B94|1|DDNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3')RESTRICTION ENDONUCLEASE ECORV WITH CALCIUMX-ray diffraction1.91999-02-26
272B0E|1|C+ 2B0E|1|D5'-D(*AP*AP*AP*GP*AP*AP*(DU)P*TP*CP*TP*T)-3'EcoRV Restriction Endonuclease/GAAUTC/Ca2+X-ray diffraction1.92005-09-27
281B97|1|C+ 1B97|1|DDNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3')ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONUCLEASE: A CATALYTIC ROLE FOR A MAIN CHAIN CARBONYL GROUPX-ray diffraction1.91999-02-26
291A1J|1|B+ 1A1J|1|CDNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3'), DNA (5'-D(*TP*AP*CP*GP*CP*CP*CP*AP*CP*GP*C)-3')RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCGT SITE)X-ray diffraction21998-06-17
301RVA|1|C+ 1RVA|1|DDNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3')MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTIONX-ray diffraction21995-01-26
312B0D|1|C+ 2B0D|1|D5'-D(*AP*AP*AP*GP*AP*AP*TP*TP*CP*TP*T)-3'EcoRV Restriction Endonuclease/GAATTC/Ca2+X-ray diffraction22005-09-27
321EO3|1|C+ 1EO3|1|DDNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3')INHIBITION OF ECORV ENDONUCLEASE BY DEOXYRIBO-3'-S-PHOSPHOROTHIOLATES: A HIGH RESOLUTION X-RAY CRYSTALLOGRAPHIC STUDYX-ray diffraction22000-04-04
331AZ0|1|C+ 1AZ0|1|DDNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3')ECORV ENDONUCLEASE/DNA COMPLEXX-ray diffraction21998-06-19
341BGB|1|C+ 1BGB|1|DDNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')ECORV ENDONUCLEASE COMPLEX WITH 5'-CGGGATATCCC DNAX-ray diffraction21998-10-28
351BSU|1|D+ 1BSU|1|CDNA (5'-D(*AP*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3'), DNA (5'-D(P*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3')STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASEX-ray diffraction21998-09-09

Release history

Release0.200.210.22
Date2011-06-042011-06-112011-06-18

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

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).
#SPDBTitleMethodResolutionLengthNAKB_NA_annotationNAKB_protein_annotation
1
3MR3|1|T+3MR3|1|P
Human DNA polymerase eta - DNA ternary complex with the 3'T of a CPD in the active site (TT1)X-RAY DIFFRACTION1.7511B-form double helix,double helix,structureenzyme,polymerase,transferase
2
1ORN|1|B+1ORN|1|C
Structure of a Trapped Endonuclease III-DNA Covalent Intermediate: Estranged-Guanine ComplexX-RAY DIFFRACTION1.711B-form double helix,double helix,structureenzyme,hydrolase,nuclease
3
1TEZ|1|I+1TEZ|1|J
COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANSX-RAY DIFFRACTION1.811enzyme,lyase
4
1TEZ|1|K+1TEZ|1|L
COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANSX-RAY DIFFRACTION1.811enzyme,lyase
5
2B0E|1|C+2B0E|1|D
EcoRV Restriction Endonuclease/GAAUTC/Ca2+X-RAY DIFFRACTION1.911B-form double helix,double helix,structureenzyme,hydrolase,nuclease
6
1RVA|1|C+1RVA|1|D
MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTIONX-RAY DIFFRACTION211B-form double helix,double helix,structureenzyme,hydrolase,nuclease
7
1AZ0|1|C+1AZ0|1|D
ECORV ENDONUCLEASE/DNA COMPLEXX-RAY DIFFRACTION211B-form double helix,double helix,structureenzyme,hydrolase,nuclease
8
1SUZ|1|C+1SUZ|1|D
The structure of K92A EcoRV bound to cognate DNA and Mg2+X-RAY DIFFRACTION1.811B-form double helix,double helix,structureenzyme,hydrolase,nuclease
9
1B94|1|C+1B94|1|D
RESTRICTION ENDONUCLEASE ECORV WITH CALCIUMX-RAY DIFFRACTION1.911B-form double helix,double helix,structureenzyme,hydrolase,nuclease
10
1BSU|1|D+1BSU|1|C
STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASEX-RAY DIFFRACTION211B-form double helix,double helix,structureenzyme,hydrolase,nuclease
11
2B0D|1|C+2B0D|1|D
EcoRV Restriction Endonuclease/GAATTC/Ca2+X-RAY DIFFRACTION211B-form double helix,double helix,structureenzyme,hydrolase,nuclease
12
1EON|1|C+1EON|1|D
ECORV BOUND TO 3'-S-PHOSPHOROTHIOLATE DNA AND CA2+X-RAY DIFFRACTION1.611B-form double helix,double helix,structureenzyme,hydrolase,nuclease
13
1B97|1|C+1B97|1|D
ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONUCLEASE: A CATALYTIC ROLE FOR A MAIN CHAIN CARBONYL GROUPX-RAY DIFFRACTION1.911B-form double helix,double helix,structureenzyme,hydrolase,nuclease
14
1EO3|1|C+1EO3|1|D
INHIBITION OF ECORV ENDONUCLEASE BY DEOXYRIBO-3'-S-PHOSPHOROTHIOLATES: A HIGH RESOLUTION X-RAY CRYSTALLOGRAPHIC STUDYX-RAY DIFFRACTION211B-form double helix,double helix,structureenzyme,hydrolase,nuclease
15
1BGB|1|C+1BGB|1|D
ECORV ENDONUCLEASE COMPLEX WITH 5'-CGGGATATCCC DNAX-RAY DIFFRACTION211B-form double helix,double helix,structureenzyme,hydrolase,nuclease
16
3GOX|1|C+3GOX|1|D
Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I in the absence of EDTAX-RAY DIFFRACTION1.511B-form double helix,double helix,structureenzyme,hydrolase,nuclease
17
3FC3|1|D
Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99IX-RAY DIFFRACTION1.7511B-form double helix,double helix,structureenzyme,hydrolase,nuclease
18
476D|1|A+476D|1|B
CALCIUM FORM OF B-DNA UNDECAMER GCGAATTCGCGX-RAY DIFFRACTION1.311B-form double helix,double helix,structure
19
1E3O|1|A+1E3O|1|B
Crystal structure of Oct-1 POU dimer bound to MOREX-RAY DIFFRACTION1.911DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription
20
3MQY|1|D+3MQY|1|F+3MQY|1|C+3MQY|1|E
SgrAI with cleaved DNA and Magnesium boundX-RAY DIFFRACTION211B-form double helix,double helix,structureenzyme,hydrolase,nuclease
21
1A1I|1|B+1A1I|1|C
RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCAC SITE)X-RAY DIFFRACTION1.611B-form double helix,double helix,structureDNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription
22
1A1K|1|B+1A1K|1|C
RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GACC SITE)X-RAY DIFFRACTION1.911B-form double helix,double helix,structureDNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription
23
1A1J|1|B+1A1J|1|C
RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCGT SITE)X-RAY DIFFRACTION211B-form double helix,double helix,structureDNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription
24
1A1G|1|B+1A1G|1|C
DSNR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCGT SITE)X-RAY DIFFRACTION1.911B-form double helix,double helix,structureDNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription
25
1JK2|1|B+1JK2|1|C
Zif268 D20A mutant bound to the GCT DNA siteX-RAY DIFFRACTION1.6511B-form double helix,double helix,structureDNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription
26
1A1H|1|B+1A1H|1|C
QGSR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCAC SITE)X-RAY DIFFRACTION1.611double helix,structureDNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription
27
1JK1|1|B+1JK1|1|C
Zif268 D20A Mutant Bound to WT DNA SiteX-RAY DIFFRACTION1.911B-form double helix,double helix,structureDNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription
28
1AAY|1|B+1AAY|1|C
ZIF268 ZINC FINGER-DNA COMPLEXX-RAY DIFFRACTION1.611B-form double helix,double helix,structureDNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription
29
1SSP|1|B+1SSP|1|A
WILD-TYPE URACIL-DNA GLYCOSYLASE BOUND TO URACIL-CONTAINING DNAX-RAY DIFFRACTION1.911B-form double helix,double helix,structureenzyme,hydrolase
30
3Q8P|1|T
Human DNA polymerase iota incorporating dCTP opposite 8-oxo-guanineX-RAY DIFFRACTION1.9529enzyme,polymerase,transferase
31
3MDC|1|T+3MDC|1|P+3MDC|1|D
DNA polymerase lambda in complex with dFdCTPX-RAY DIFFRACTION1.99911enzyme,polymerase,transferase
32
2PFN|1|T+2PFN|1|P+2PFN|1|D
Na in the active site of DNA Polymerase lambdaX-RAY DIFFRACTION1.911enzyme,polymerase,transferase
33
1XSN|1|T+1XSN|1|P+1XSN|1|D
Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddTTPX-RAY DIFFRACTION1.9511enzyme,polymerase,transferase
34
2PFO|1|T+2PFO|1|P+2PFO|1|D
DNA Polymerase lambda in complex with DNA and dUPNPPX-RAY DIFFRACTION211enzyme,polymerase,transferase
35
3PNC|1|C+3PNC|1|B+3PNC|1|D
Ternary crystal structure of a polymerase lambda variant with a GT mispair at the primer terminus and sodium at catalytic metal siteX-RAY DIFFRACTION211enzyme,polymerase,transferase

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