SMTL ID : 5vrw.1

Human DNA polymerase beta pre-catalytic 8-oxoG:dC extension complex with dTTP bound in non-planar conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 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: 17 residues within 4Å: Chain A: C.2, G.3, A.4, C.5 Chain C: K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69, K.72 Ligands: CA.5 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.37, C:R.283 pi-Stacking: C:H.34

7 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: TTP.4 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.190, C:D.192, C:D.256 CA.3: 4 residues within 4Å: Chain B: C.9 Chain C: T.101, V.103, I.106 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.101, C:V.103, C:I.106, H2O.1 CA.5: 4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:K.60, C:L.62, C:V.65 CA.6: 3 residues within 4Å: Chain C: D.190, D.192 Ligands: TTP.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.190, C:D.192 CA.7: 2 residues within 4Å: Chain C: D.314, D.318 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.314, C:D.318 CA.8: 1 residues within 4Å: Chain C: E.249 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.249 CA.9: 1 residues within 4Å: Chain C: E.335 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.335

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.4: 19 residues within 4Å: Chain A: A.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, S.275, D.276, N.279 Ligands: CA.2, CA.6 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:D.276 Hydrogen bonds: C:S.180, C:S.180, C:R.183, C:G.189, C:D.190, C:D.190, C:Y.271, C:N.279 Salt bridges: C:R.149, C:R.183

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 5 residues within 4Å: Chain C: I.174, T.176, T.196, Y.265, Y.266 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.174, C:T.176, C:Y.266, C:Y.266 PEG.11: 2 residues within 4Å: Chain C: E.9, L.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reed, A.J. et al., Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta. J. Am. Chem. Soc. (2017)

Release Date

2017-07-19

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

Related Entries With Identical Sequence