SMTL ID : 4r63.1

Binary complex crystal structure of R258A mutant of DNA polymerase Beta

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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: 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 B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.34 pi-Stacking: A:H.34

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

NA.2: 7 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, I.106 Chain C: G.9 Ligands: NA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106 NA.3: 5 residues within 4Å: Chain A: K.60, L.62, G.64, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.62, A:G.64, A:V.65 NA.4: 2 residues within 4Å: Chain A: T.101 Ligands: NA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.101 Water bridges: A:K.27 NA.5: 1 residues within 4Å: Chain A: S.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.171 Water bridges: A:D.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beard, W.A. et al., Substrate-induced DNA Polymerase beta Activation. J.Biol.Chem. (2014)

Release Date

2014-10-08

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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