SMTL ID : 5vry.1

Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 20 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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: 17 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 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.280, C:R.283 Water bridges: C:N.37, C:N.37, C:N.37, C:R.40, C:K.280 Salt bridges: C:K.280 pi-Stacking: C:H.34

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

MG.2: 1 residues within 4Å: Chain A: G.8 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: T.11 Ligands: TTP.3, PPV.8 No protein-ligand interaction detected (PLIP) MG.5: 7 residues within 4Å: Chain B: C.10, T.11 Chain C: D.190, D.192, D.256 Ligands: TTP.3, MG.6 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.190, C:D.192, C:D.256, H2O.2 MG.6: 6 residues within 4Å: Chain B: T.11 Chain C: D.190, D.192 Ligands: TTP.3, MG.5, PPV.8 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H2O.6 MG.7: 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.10 MG.9: 1 residues within 4Å: Chain C: E.249 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.249, C:E.249, H2O.3, H2O.9, H2O.11

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.3: 21 residues within 4Å: Chain A: A.6 Chain B: C.10, T.11 Chain C: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, D.276, N.279 Ligands: MG.4, MG.5, MG.6, PPV.8 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:D.276 Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:S.180, C:R.183, C:G.189, C:D.190, C:N.279 Water bridges: C:F.181, C:F.181, C:D.276, C:D.276 Salt bridges: C:R.183

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.8: 11 residues within 4Å: Chain B: T.11 Chain C: R.149, G.179, S.180, R.183, S.188, G.189, D.192 Ligands: TTP.3, MG.4, MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.180, C:S.180, C:S.180, C:G.189, C:D.192 Water bridges: C:R.149, C:R.149, C:F.181, C:F.181, C:R.183, C:R.183 Salt bridges: C:R.149, C:R.183

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 2 residues within 4Å: Chain C: T.205, E.232 Ligand excluded by PLIP

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.11: 3 residues within 4Å: Chain C: I.174, T.196, Y.265 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.196 pi-Stacking: C:Y.265

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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