- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- monomer
- Ligands
- 1 x DG- DT- DC- DG- DG: 5-MER PHOSPHORYLATED DOWNSTREAM PRIME(Non-covalent)
- 1 x 1RZ: Lamivudine Triphosphate(Non-covalent)
1RZ.2: 16 residues within 4Å:- Chain A: G.181, S.182, R.185, S.190, G.191, D.192, D.194, Y.273, F.274, G.276, D.278, N.281
- Chain B: C.10
- Chain C: G.6
- Ligands: MN.6, MN.7
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:D.278
- Hydrogen bonds: A:R.151, A:S.182, A:S.182, A:G.191, A:D.192, A:N.281
- Water bridges: A:R.185, A:R.185
- Salt bridges: A:R.185
- 6 x MN: MANGANESE (II) ION(Non-covalent)
MN.3: 2 residues within 4Å:- Chain A: H.339, H.341
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:H.339, A:H.341, H2O.1, H2O.6
MN.4: 2 residues within 4Å:- Chain A: E.119
- Ligands: ACT.18
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:E.119
MN.5: 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.6: 4 residues within 4Å:- Chain A: D.192, D.194
- Ligands: 1RZ.2, MN.7
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.192, A:D.194, H2O.2
MN.7: 6 residues within 4Å:- Chain A: D.192, D.194, D.258
- Chain B: C.10
- Ligands: 1RZ.2, MN.6
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.192, A:D.194, A:D.258, H2O.3, H2O.4
MN.8: 2 residues within 4Å:- Chain A: H.287, E.290
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:H.287, A:E.290
- 5 x NA: SODIUM ION(Non-functional Binders)
NA.9: 1 residues within 4Å:- Chain A: D.132
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.132
NA.10: 2 residues within 4Å:- Chain A: D.147, H.254
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.147, A:H.254, A:H.254
NA.11: 4 residues within 4Å:- Chain A: K.62, L.64, V.67
- Ligands: DG-DT-DC-DG-DG.1
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.62, A:G.66, A:V.67
NA.12: 5 residues within 4Å:- Chain A: T.103, V.105, S.106, 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.13: 2 residues within 4Å:- Chain A: D.93
- Ligands: ACT.17
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.93
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x ACT: ACETATE ION(Non-functional Binders)
ACT.16: 8 residues within 4Å:- Chain A: H.36, N.39, A.40, K.43, K.282
- Chain C: C.5, G.6
- Ligands: DG-DT-DC-DG-DG.1
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:N.39, A:A.40
- Water bridges: A:N.39
- Salt bridges: A:K.43, A:K.282
ACT.17: 3 residues within 4Å:- Chain A: V.31, D.93
- Ligands: NA.13
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:V.31
- Water bridges: A:D.93, A:S.96, A:S.96, A:S.96
ACT.18: 3 residues within 4Å:- Chain A: D.118, E.119
- Ligands: MN.4
No protein-ligand interaction detected (PLIP)ACT.19: 3 residues within 4Å:- Chain A: K.29, Y.38
- Chain B: C.10
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:K.29
ACT.20: 1 residues within 4Å:- Chain A: K.129
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:K.129
ACT.21: 2 residues within 4Å:- Chain A: N.247, D.248
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.248, A:D.248
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Reed, A.J. et al., Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc. (2017)
- Release Date
- 2017-01-11
- Peptides
- DNA polymerase beta: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- monomer
- Ligands
- 1 x DG- DT- DC- DG- DG: 5-MER PHOSPHORYLATED DOWNSTREAM PRIME(Non-covalent)
- 1 x 1RZ: Lamivudine Triphosphate(Non-covalent)
- 6 x MN: MANGANESE (II) ION(Non-covalent)
- 5 x NA: SODIUM ION(Non-functional Binders)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x ACT: ACETATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Reed, A.J. et al., Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc. (2017)
- Release Date
- 2017-01-11
- Peptides
- DNA polymerase beta: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A