SMTL ID : 7rbg.1

Human DNA polymerase beta crosslinked ternary complex 1

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(*GP*TP*CP*GP*G)-3')(Non-covalent)

DG-DT-DC-DG-DG.1: 20 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 Ligands: QPJ.3, CA.5, NA.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.34, C:R.283, C:R.283 Salt bridges: C:K.280

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

DCP.2: 18 residues within 4Å: Chain A: G.6 Chain B: C.10 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: CA.4, NA.7 13 PLIP interactions: 13 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:R.149, C:R.149, C:D.276 Salt bridges: C:R.183

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

QPJ.3: 5 residues within 4Å: Chain C: K.35, Y.39, K.68, K.72 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.72 Hydrogen bonds: C:K.68 Salt bridges: C:K.35

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain C: D.190, D.192 Ligands: DCP.2, NA.7 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H2O.7 CA.5: 4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:K.60, C:L.62, C:V.65, H2O.2, H2O.8 CA.6: 4 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, 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.9

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

NA.7: 6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: DCP.2, CA.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.256 NA.8: 4 residues within 4Å: Chain C: A.38, K.41, G.64 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.42, C:G.64

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

CL.9: 4 residues within 4Å: Chain C: A.32, I.33, H.34, K.35 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: C.5 Chain C: H.34, N.37 Ligand excluded by 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: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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