SMTL ID : 5v1p.1

DNA polymerase beta substrate complex with 8-oxoG:C at the primer terminus and incoming dCTP analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

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

DG-DT-DC-DG-DG.1: 18 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: NA.4 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.279, C:R.283, C:R.283 Water bridges: C:N.37, C:N.37 pi-Stacking: C:H.34

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

NA.2: 6 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, G.105, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.103, C:G.105, C:I.106 NA.4: 5 residues within 4Å: Chain C: K.60, L.62, G.64, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.60, C:G.64, C:V.65

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain B: G.10 Chain C: D.190, D.192, D.256 Ligands: XC5.5, MG.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, C:D.256, H2O.2 MG.10: 4 residues within 4Å: Chain C: D.190, D.192 Ligands: MG.3, XC5.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H2O.7

1 x XC5: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine(Non-covalent)

XC5.5: 18 residues within 4Å: Chain A: G.6 Chain B: G.10 Chain C: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, S.275, D.276, N.279 Ligands: MG.3, MG.10 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:D.276 Hydrogen bonds: C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:D.190, C:N.279 Water bridges: C:R.40, C:R.149, C:R.149, C:R.149, C:S.180, C:D.190, C:D.190, C:R.254, C:R.254, C:R.254, C:D.276

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

CL.6: 6 residues within 4Å: Chain C: D.263, Q.264, Y.265, Y.266, C.267, V.313 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain C: A.32, I.33, H.34, K.35 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: K.81, L.82, E.86 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain C: N.294, Y.296, T.297, R.299 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whitaker, A.M. et al., Capturing a mammalian DNA polymerase extending from an oxidized nucleotide. Nucleic Acids Res. (2017)

Release Date

2017-05-10

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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