SMTL ID : 5vs4.1

Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 120 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 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: C.1, C.2, G.3, A.4, C.5 Chain C: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69, E.288 Ligands: MG.7 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.280, C:R.283 Water bridges: C:N.37, C:N.37 Salt bridges: C:K.280 pi-Stacking: C:H.34

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: T.11 Ligands: PPV.3 No protein-ligand interaction detected (PLIP) MG.4: 6 residues within 4Å: Chain B: A.10, T.11 Chain C: D.190, D.192, D.256 Ligands: MG.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.190, C:D.190, C:D.192, C:D.256 MG.5: 5 residues within 4Å: Chain B: T.11 Chain C: D.190, D.192 Ligands: PPV.3, MG.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H2O.8 MG.6: 6 residues within 4Å: Chain B: C.9 Chain C: T.101, V.103, S.104, G.105, I.106 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.101, C:V.103, C:I.106, H2O.2, H2O.11 MG.7: 4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:K.60, C:L.62, C:V.65, H2O.3, H2O.12 MG.8: 1 residues within 4Å: Chain C: E.249 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.249, H2O.4, H2O.9, H2O.10, H2O.13

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3: 11 residues within 4Å: Chain B: T.11 Chain C: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192 Ligands: MG.2, MG.5 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.180, C:S.180, C:G.189, C:D.190 Water bridges: C:S.180, C:D.190 Salt bridges: C:R.149, C:R.183

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 4 residues within 4Å: Chain C: I.174, T.196, K.262, Y.265 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.174, C:T.196, C:Y.265 Hydrogen bonds: C:T.196, C:T.196 Salt bridges: C:K.262 ACT.10: 5 residues within 4Å: Chain C: F.200, T.205, E.232, T.233, L.259 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:E.232, C:T.233 Hydrogen bonds: C:E.232 Water bridges: C:K.209, C:L.210, C:L.210 ACT.11: 2 residues within 4Å: Chain C: R.152, L.156 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.156 Salt bridges: C:R.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reed, A.J. et al., Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta. J. Am. Chem. Soc. (2017)

Release Date

2017-07-19

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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