SMTL ID : 6uom.1

Y271G DNA polymerase beta ternary complex with templating adenine and incoming r8-oxo-GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x DG- DC- DT- DG- DA- DT- DG- DC- DG: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*G)-3')(Non-covalent)

DG-DC-DT-DG-DA-DT-DG-DC-DG.1: 20 residues within 4Å: Chain A: C.8, G.9, C.10, A.11, T.12, C.13, A.14, G.15, C.16 Chain B: V.103, S.104, G.105, I.106, G.107, P.108, S.109, A.110, K.234 Ligands: DOC.4, NA.6 Protein-ligand interaction information (PLIP) not available

1 x DG- DT- DC- DG- DG: DNA (5'-D(P*GP*TP*CP*GP*G)-3')(Non-covalent)

DG-DT-DC-DG-DG.2: 20 residues within 4Å: Chain A: C.1, C.2, G.3, A.4, C.5 Chain B: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69 Ligands: EDO.3, EDO.5, NA.7 Protein-ligand interaction information (PLIP) not available

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: C.2, G.3 Ligands: DG-DT-DC-DG-DG.2 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain B: K.35, K.68 Ligands: DG-DT-DC-DG-DG.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.35, B:K.35

1 x DOC: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DOC.4: 5 residues within 4Å: Chain A: A.6, G.7 Chain B: R.254 Ligands: DG-DC-DT-DG-DA-DT-DG-DC-DG.1, 8GT.12 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.190, B:R.254, B:R.254 Salt bridges: B:R.254

4 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain B: T.101, V.103, I.106 Ligands: DG-DC-DT-DG-DA-DT-DG-DC-DG.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.105, B:I.106, B:I.106 NA.7: 4 residues within 4Å: Chain B: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.60, B:V.65 Water bridges: B:K.60 NA.10: 2 residues within 4Å: Chain B: D.145, H.252 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.145, B:H.252, B:H.252 NA.11: 1 residues within 4Å: Ligands: 8GT.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.189

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.8: 4 residues within 4Å: Chain B: D.190, D.192 Ligands: MN.9, 8GT.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.190, B:D.192, H2O.4 MN.9: 5 residues within 4Å: Chain B: D.190, D.192, D.256 Ligands: MN.8, 8GT.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.190, B:D.192, H2O.2

1 x 8GT: 8-OXO-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

8GT.12: 21 residues within 4Å: Chain A: A.6, G.7 Chain B: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192, G.271, F.272, T.273, G.274, S.275, D.276, N.279 Ligands: DOC.4, MN.8, MN.9, NA.11 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.180, B:S.180, B:R.183, B:G.189, B:D.190, B:G.271, B:F.272, B:N.279 Water bridges: B:R.283 Salt bridges: B:R.149, B:R.183, B:D.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, M.R. et al., Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta. J.Biol.Chem. (2020)

Release Date

2020-01-08

Peptides

DNA polymerase beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA polymerase beta

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