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SMTL ID : 3rje.1

Ternary complex of DNA Polymerase Beta with a gapped DNA containing 8odG at template position

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69, K.72
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:	6 residues within 4Å: Chain A: T.101, V.103, S.104, I.106 Chain C: G.9 Ligands: NA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106
NA.3:	4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.62, A:V.65
NA.4:	2 residues within 4Å: Chain A: T.101 Ligands: NA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.101 Water bridges: A:K.27, 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, A:S.171

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Batra, V.K. et al., Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-01-18

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

DNA polymerase beta

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