SMTL ID : 7rbe.1

Human DNA polymerase beta crosslinked binary complex - A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 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, 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, NA.5 2 PLIP interactions: 2 interactions with chain A 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.72 Water bridges: A:Y.39, A:K.68, A:K.72 Salt bridges: A:K.35, A:K.84

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

NA.3: 4 residues within 4Å: Chain A: T.101, V.103, I.106 Chain B: G.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.106, A:I.106 NA.4: 6 residues within 4Å: Chain A: N.28, V.29, Q.31, I.97, P.108, R.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.31, A:R.112, A:R.112 NA.5: 4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.65, A:V.65 NA.6: 5 residues within 4Å: Chain A: I.150, E.154, M.158, L.241, R.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.253, A:R.253

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.7: 7 residues within 4Å: Chain A: R.149, G.179, S.180, R.183, S.188, G.189, D.190 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:G.189, A:D.190 Water bridges: A:F.181, A:F.181, A:F.272 Salt bridges: A:R.149, A:R.183 CIT.8: 2 residues within 4Å: Chain A: H.134, R.137 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.134 Salt bridges: A:H.134, A:R.137, A:K.141

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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