SMTL ID : 4rq7.1

Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dATP soaked with MgCl2 for 1hr

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 19 residues within 4Å: Chain A: H.36, K.37, A.40, Y.41, L.64, P.65, G.66, V.67, G.68, T.69, K.70, I.71 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: NA.3, ACT.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.36 pi-Stacking: A:H.36

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

NA.2: 4 residues within 4Å: Chain A: T.103, V.105, I.108 Chain B: G.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.108, A:I.108 NA.3: 4 residues within 4Å: Chain A: K.62, L.64, V.67 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.66, A:V.67, A:V.67 NA.6: 1 residues within 4Å: Ligands: ACT.9 No protein-ligand interaction detected (PLIP) NA.8: 1 residues within 4Å: Chain C: A.14 No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain A: N.296, T.299, R.301 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: A.34, I.35, H.36, K.37 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 2 residues within 4Å: Chain B: T.3, G.4 No protein-ligand interaction detected (PLIP) ACT.9: 4 residues within 4Å: Chain C: G.3, A.4 Ligands: DG-DT-DC-DG-DG.1, NA.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vyas, R. et al., Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography. J.Am.Chem.Soc. (2015)

Release Date

2015-04-15

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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