Equivalence class DNA_2.0_04418.2 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1NK0|1|C+ 1NK0|1|B (rep) | DNA TEMPLATE STRAND, DNA PRIMER STRAND | ADENINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.7 | 2004-03-30 | ||||
| 2 | 3MFI|1|T+ 3MFI|1|P | 5'-D(*TP*AP*AP*(TTD)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' | DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer | X-ray diffraction | 1.76 | 2010-06-23 | ||||
| 3 | 1U4B|1|C+ 1U4B|1|B | DNA template strand with 8-oxoguanine, DNA primer strand | Extension of an adenine-8oxoguanine mismatch | X-ray diffraction | 1.6 | 2004-09-14 | ||||
| 4 | 1NKC|1|B+ 1NKC|1|C | DNA PRIMER STRAND, DNA TEMPLATE STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND DATP. | X-ray diffraction | 1.8 | 2004-03-30 | ||||
| 5 | 1NK8|1|C+ 1NK8|1|B | DNA TEMPLATE STRAND, DNA PRIMER STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP. | X-ray diffraction | 1.9 | 2004-03-30 | ||||
| 6 | 1NJX|1|C+ 1NJX|1|B | DNA TEMPLATE STRAND, DNA PRIMER STRAND | THYMINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.65 | 2004-03-30 | ||||
| 7 | 1NK7|1|C+ 1NK7|1|B | DNA TEMPLATE STRAND, DNA PRIMER STRAND | GUANINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.9 | 2004-03-30 | ||||
| 8 | 3FDQ|1|C+ 3FDQ|1|D | 5'-D(*AP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*AP*AP*T)-3', 5'-D(*TP*AP*TP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*A)-3' | Recognition of AT-rich DNA binding sites by the MogR Repressor | X-ray diffraction | 1.75 | 2009-06-02 | ||||
| 9 | 1RH6|1|C+ 1RH6|1|D | 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3', 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3' | Bacteriophage Lambda Excisionase (Xis)-DNA Complex | X-ray diffraction | 1.7 | 2004-06-29 | ||||
| 10 | 1NK9|1|C+ 1NK9|1|B | DNA TEMPLATE STRAND, DNA PRIMER STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER TWO ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP AND DGTP. | X-ray diffraction | 1.9 | 2004-03-30 | ||||
| 11 | 1NJW|1|C+ 1NJW|1|B | DNA TEMPLATE STRAND, DNA PRIMER STRAND | GUANINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.9 | 2004-03-30 | ||||
| 12 | 2HHQ|1|C+ 2HHQ|1|B | 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*TP*AP*TP*GP*A)-3', 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3' | O6-methyl-guanine:T pair in the polymerase-10 basepair position | X-ray diffraction | 1.8 | 2006-12-12 | ||||
| 13 | 1NKB|1|C+ 1NKB|1|B | DNA TEMPLATE STRAND, DNA PRIMER STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, AND DTTP. | X-ray diffraction | 2 | 2004-03-30 | ||||
| 14 | 2XHI|1|B+ 2XHI|1|C | 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3', 5'-D(*GP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' | Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA glycosylase | X-ray diffraction | 1.55 | 2011-01-26 | ||||
| 15 | 1U47|1|C+ 1U47|1|B | DNA template strand with 8-oxoguanine, DNA primer strand | cytosine-8-Oxoguanine base pair at the polymerase active site | X-ray diffraction | 2 | 2004-09-14 | ||||
| 16 | 1XC9|1|C+ 1XC9|1|B | DNA template strand with benzo[a]pyrene adduct, DNA primer strand | Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication | X-ray diffraction | 1.9 | 2004-12-14 | ||||
| 17 | 3IAG|1|A+ 3IAG|1|B | 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*AP*CP*AP*CP*GP*AP*T)-3', 5'-D(*TP*TP*AP*TP*CP*GP*TP*GP*TP*GP*AP*AP*AP*GP*A)-3' | CSL (RBP-Jk) bound to HES-1 nonconsensus site | X-ray diffraction | 2 | 2009-11-10 | ||||
| 18 | 1M3Q|1|B+ 1M3Q|1|C | 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3', 5'-D(*GP*CP*GP*TP*CP*CP*AP*(DRZ)P*GP*TP*CP*TP*AP*CP*C)-3' | Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine | X-ray diffraction | 1.9 | 2004-02-17 | ||||
| 19 | 1DSZ|1|C+ 1DSZ|1|D | DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3'), DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*G)-3') | STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1 | X-ray diffraction | 1.7 | 2000-07-10 |
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 |
|---|
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 | 1DSZ|1|C+1DSZ|1|D | STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1 | X-RAY DIFFRACTION | 1.7 | 15 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 2 | 3IAG|1|A+3IAG|1|B | CSL (RBP-Jk) bound to HES-1 nonconsensus site | X-RAY DIFFRACTION | 2 | 15 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription |
| 3 | 1XC9|1|C+1XC9|1|B | Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication | X-RAY DIFFRACTION | 1.9 | 15 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 4 | 2HHQ|1|C+2HHQ|1|B | O6-methyl-guanine:T pair in the polymerase-10 basepair position | X-RAY DIFFRACTION | 1.8 | 15 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 5 | 1NKC|1|B+1NKC|1|C | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND DATP. | X-RAY DIFFRACTION | 1.8 | 15 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase |
| 6 | 1U47|1|C+1U47|1|B | cytosine-8-Oxoguanine base pair at the polymerase active site | X-RAY DIFFRACTION | 2 | 15 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 7 | 1RH6|1|C+1RH6|1|D | Bacteriophage Lambda Excisionase (Xis)-DNA Complex | X-RAY DIFFRACTION | 1.7 | 15 | B-form double helix,double helix,structure | enzyme,recombinase |
| 8 | 1NJW|1|C+1NJW|1|B | GUANINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.9 | 15 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase |
| 9 | 1NJX|1|C+1NJX|1|B | THYMINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.65 | 15 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase |
| 10 | 3FDQ|1|C+3FDQ|1|D | Recognition of AT-rich DNA binding sites by the MogR Repressor | X-RAY DIFFRACTION | 1.75 | 15 | B-form double helix,double helix,structure | regulatory,transcription |
| 11 | 1NK9|1|C+1NK9|1|B | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER TWO ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP AND DGTP. | X-RAY DIFFRACTION | 1.9 | 15 | double helix,feature,mispair,structure | enzyme,polymerase,transferase |
| 12 | 1NKB|1|C+1NKB|1|B | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, AND DTTP. | X-RAY DIFFRACTION | 2 | 15 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase |
| 13 | 1U4B|1|C+1U4B|1|B | Extension of an adenine-8oxoguanine mismatch | X-RAY DIFFRACTION | 1.6 | 15 | enzyme,polymerase,transferase | |
| 14 | 1NK8|1|C+1NK8|1|B | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP. | X-RAY DIFFRACTION | 1.9 | 15 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase |
| 15 | 1NK0|1|C+1NK0|1|B | ADENINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.7 | 15 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase |
| 16 | 3MFI|1|T+3MFI|1|P | DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer | X-RAY DIFFRACTION | 1.76 | 15 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 17 | 1NK7|1|C+1NK7|1|B | GUANINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.9 | 15 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 18 | 1M3Q|1|B+1M3Q|1|C | Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine | X-RAY DIFFRACTION | 1.9 | 15 | B-form double helix,double helix,structure | enzyme,hydrolase |
| 19 | 2XHI|1|B+2XHI|1|C | Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA glycosylase | X-RAY DIFFRACTION | 1.55 | 15 | B-form double helix,double helix,structure | enzyme,hydrolase |
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