- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- monomer
- Ligands
- 1 x DG- DT- DC- DG- DG: DNA (5'-D(P*GP*TP*CP*GP*G)-3')(Non-covalent)
- 1 x PPV: PYROPHOSPHATE(Non-covalent)
- 6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)
MN.3: 5 residues within 4Å:- Chain A: D.192, D.194
- Chain B: C.11
- Ligands: PPV.2, MN.4
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.192, A:D.194, H2O.4
MN.4: 6 residues within 4Å:- Chain A: D.192, D.194, D.258
- Chain B: C.10, C.11
- Ligands: MN.3
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.192, A:D.192, A:D.194, A:D.258, H2O.4
MN.5: 2 residues within 4Å:- Chain A: H.339, H.341
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:H.339, A:H.341, H2O.1, H2O.4, H2O.4
MN.6: 3 residues within 4Å:- Chain A: K.50, H.338, H.340
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:K.50, A:H.338, A:H.340, H2O.4
MN.7: 1 residues within 4Å:- Chain A: H.343
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:H.343, H2O.1, H2O.5
MN.16: 2 residues within 4Å:- Chain B: C.11
- Ligands: PPV.2
No protein-ligand interaction detected (PLIP)- 7 x NA: SODIUM ION(Non-functional Binders)
NA.8: 2 residues within 4Å:- Chain A: D.147, H.254
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.254
NA.9: 4 residues within 4Å:- Chain A: T.103, V.105, I.108
- Chain B: G.9
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:G.107, A:I.108, A:I.108
NA.10: 2 residues within 4Å:- Chain A: H.287, E.290
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:H.287, A:E.290
NA.11: 1 residues within 4Å:- Chain A: D.316
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.316, A:D.316
NA.12: 4 residues within 4Å:- Chain A: K.62, L.64, V.67
- Ligands: DG-DT-DC-DG-DG.1
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.64, A:V.67
NA.13: 3 residues within 4Å:- Chain A: T.12, N.14, H.342
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.14, A:H.342
- Water bridges: A:K.54
NA.17: 1 residues within 4Å:- Chain C: A.11
No protein-ligand interaction detected (PLIP)- 3 x ACT: ACETATE ION(Non-functional Binders)
ACT.14: 4 residues within 4Å:- Chain C: A.4, C.5
- Ligands: DG-DT-DC-DG-DG.1, DG-DT-DC-DG-DG.1
No protein-ligand interaction detected (PLIP)ACT.15: 2 residues within 4Å:- Ligands: DG-DT-DC-DG-DG.1, DG-DT-DC-DG-DG.1
No protein-ligand interaction detected (PLIP)ACT.18: 3 residues within 4Å:- Chain C: C.2, G.3, A.4
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Vyas, R. et al., Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography. J.Am.Chem.Soc. (2015)
- Release Date
- 2015-04-15
- Peptides
- DNA polymerase beta: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- monomer
- Ligands
- 1 x DG- DT- DC- DG- DG: DNA (5'-D(P*GP*TP*CP*GP*G)-3')(Non-covalent)
- 1 x PPV: PYROPHOSPHATE(Non-covalent)
- 6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)
- 7 x NA: SODIUM ION(Non-functional Binders)
- 3 x ACT: ACETATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Vyas, R. et al., Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography. J.Am.Chem.Soc. (2015)
- Release Date
- 2015-04-15
- Peptides
- DNA polymerase beta: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A