SMTL ID : 7rbm.1

Human DNA polymerase beta crosslinked complex, 60 s Ca to Mn exchange

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

monomer

Ligands

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

DG-DT-DC-DG-DG.1: 17 residues within 4Å: Chain A: H.34, K.35, A.38, Y.39, P.63, G.64, V.65, G.66, T.67, K.68, I.69 Chain C: C.2, G.3, A.4, C.5 Ligands: QPJ.2, MN.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.283, A:R.283 Salt bridges: A:K.280 pi-Stacking: A:H.34

1 x QPJ: 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol(Covalent)

QPJ.2: 6 residues within 4Å: Chain A: E.26, K.35, Y.39, K.68, K.72 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.72 Hydrogen bonds: A:K.68 Salt bridges: A:K.35

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3: 11 residues within 4Å: Chain A: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192 Chain B: C.11 Ligands: MN.5, MN.13 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.180, A:S.180, A:S.180, A:G.189, A:D.190 Water bridges: A:D.190 Salt bridges: A:R.149, A:R.183

11 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.4: 6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain B: C.10, C.11 Ligands: MN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H2O.3 MN.5: 5 residues within 4Å: Chain A: D.190, D.192 Chain B: C.11 Ligands: PPV.3, MN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.2 MN.6: 2 residues within 4Å: Chain A: K.60 Ligands: DG-DT-DC-DG-DG.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:K.60, H2O.1, H2O.2, H2O.3 MN.7: 2 residues within 4Å: Chain A: H.285, E.288 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.285, A:E.288 MN.8: 5 residues within 4Å: Chain A: T.101, V.103, S.104, I.106 Chain B: G.9 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.101, A:V.103, A:I.106, H2O.3, H2O.3 MN.9: 1 residues within 4Å: Chain A: E.117 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.117 MN.10: 3 residues within 4Å: Chain A: K.48, H.336, H.338 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:K.48, A:H.336, A:H.338 MN.11: 1 residues within 4Å: Chain A: H.337 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.337, H2O.3, H2O.3 MN.12: 1 residues within 4Å: Chain A: D.130 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.130, A:D.130 MN.13: 2 residues within 4Å: Chain B: C.11 Ligands: PPV.3 No protein-ligand interaction detected (PLIP) MN.14: 1 residues within 4Å: Chain C: G.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Interlocking activities of DNA polymerase beta in the base excision repair pathway. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-03-09

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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