SMTL ID : 4rq2.1

Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MnCl2 for 35 s

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)

DG-DT-DC-DG-DG.1: 19 residues within 4Å: Chain A: H.36, K.37, A.40, Y.41, L.64, P.65, G.66, V.67, G.68, T.69, K.70, I.71 Chain C: C.2, G.3, A.4, C.5 Ligands: NA.12, ACT.14, ACT.15 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.232, A:T.235, A:K.236, A:K.236, A:K.236, A:Y.273, A:K.282, A:R.285 Water bridges: A:H.36, A:S.231, A:K.236, A:R.285, A:F.293, A:I.295 pi-Stacking: A:H.36

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.2: 11 residues within 4Å: Chain A: R.151, G.181, S.182, R.185, S.190, G.191, D.192, D.194 Chain B: C.11 Ligands: MN.3, MN.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:G.191, A:D.192 Salt bridges: A:R.151, A:R.185

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

DNA polymerase beta

Related Entries With Identical Sequence