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SMTL ID : 5v1j.1

DNA polymerase beta open product complex with 8-oxoG:C and inserted dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 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: 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

1 PLIP interactions:

1 interactions with chain A

pi-Stacking: A:H.34

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

NA.2:	5 residues within 4Å: Chain A: T.101, V.103, S.104, I.106 Chain C: G.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.103, A:I.106
NA.3:	5 residues within 4Å: Chain A: K.60, K.61, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.62

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: 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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