Equivalence class DNA_4.0_21704.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2AGQ|1|C+ 2AGQ|1|B (rep) | 5'-D(*TP*CP*AP*TP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3', 5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*(DOC))-3' | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.1 | 2005-09-06 | ||||
| 2 | 1S10|1|C+ 1S10|1|B | 5'-D(*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3' | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-ray diffraction | 2.1 | 2004-03-30 | ||||
| 3 | 1S0O|1|D+ 1S0O|1|C | 5'-D(*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3' | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-ray diffraction | 2.1 | 2004-03-30 | ||||
| 4 | 1S0O|1|F+ 1S0O|1|E | 5'-D(*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3' | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-ray diffraction | 2.1 | 2004-03-30 | ||||
| 5 | 2IA6|1|D+ 2IA6|1|C | 5'-D(*TP*CP*AP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*A)-3' | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | X-ray diffraction | 2.5 | 2007-09-11 | ||||
| 6 | 2IA6|1|F+ 2IA6|1|E | 5'-D(*TP*CP*AP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*A)-3' | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | X-ray diffraction | 2.5 | 2007-09-11 | ||||
| 7 | 1N56|1|D+ 1N56|1|C | 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3' | synthetic construct | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | X-ray diffraction | 2.4 | 2004-02-24 | |||
| 8 | 1N56|1|F+ 1N56|1|E | 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3' | synthetic construct | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | X-ray diffraction | 2.4 | 2004-02-24 | |||
| 9 | 2AGO|1|C+ 2AGO|1|B | DNA (5'-D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3') | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.85 | 2005-09-06 | ||||
| 10 | 2AGP|1|D+ 2AGP|1|C | DNA (5'-D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC)-3') | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.9 | 2005-09-06 | ||||
| 11 | 2AGP|1|F+ 2AGP|1|E | DNA (5'-D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC)-3') | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.9 | 2005-09-06 |
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 | 1S0O|1|D+1S0O|1|C | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-RAY DIFFRACTION | 2.1 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 2 | 2IA6|1|D+2IA6|1|C | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | X-RAY DIFFRACTION | 2.5 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 3 | 1N56|1|D+1N56|1|C | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | X-RAY DIFFRACTION | 2.4 | 17 | enzyme,polymerase,transferase | |
| 4 | 2AGO|1|C+2AGO|1|B | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-RAY DIFFRACTION | 2.85 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 5 | 2AGP|1|F+2AGP|1|E | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-RAY DIFFRACTION | 2.9 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 6 | 2AGP|1|D+2AGP|1|C | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-RAY DIFFRACTION | 2.9 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 7 | 1S10|1|C+1S10|1|B | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-RAY DIFFRACTION | 2.1 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 8 | 2AGQ|1|C+2AGQ|1|B | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-RAY DIFFRACTION | 2.1 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 9 | 1N56|1|F+1N56|1|E | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | X-RAY DIFFRACTION | 2.4 | 17 | enzyme,polymerase,transferase | |
| 10 | 2IA6|1|F+2IA6|1|E | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | X-RAY DIFFRACTION | 2.5 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 11 | 1S0O|1|F+1S0O|1|E | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-RAY DIFFRACTION | 2.1 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
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