SMTL ID : 7rbj.1

Human DNA polymerase beta crosslinked complex, 30 s Ca to Mg exchange

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 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: 18 residues within 4Å: Chain A: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: QPJ.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.283, A:R.283 Water bridges: A:N.37 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: K.35, Y.39, K.68, K.72, K.84 Ligands: DG-DT-DC-DG-DG.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.72 Hydrogen bonds: A:K.68 Water bridges: A:K.84, A:K.84 Salt bridges: A:K.35, A:K.68, A:K.84

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: DCP.4, MG.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.180, A:S.180, A:G.189, A:D.190 Water bridges: A:R.149, A:R.149, A:D.190 Salt bridges: A:R.149, A:R.183

2 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)(Non-functional Binders)

DCP.4: 20 residues within 4Å: Chain A: 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 Chain B: C.10, C.11 Chain C: G.6 Ligands: PPV.3, MG.5, MG.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.276 Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:G.189, A:D.190, A:D.192, A:N.279 Salt bridges: A:R.149, A:R.183 DCP.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: D.190, D.192 Chain B: C.11 Ligands: PPV.3, DCP.4, MG.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.1 MG.6: 7 residues within 4Å: Chain A: D.190, D.192, D.256 Chain B: C.10, C.11 Ligands: DCP.4, MG.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.190, A:D.192, A:D.256, H2O.2 MG.7: 1 residues within 4Å: Chain A: T.101 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.101, H2O.1, H2O.1, H2O.5 MG.8: 3 residues within 4Å: Chain A: R.182, Y.266, E.316 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.316, H2O.5

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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