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SMTL ID : 1mq3.1

Human DNA Polymerase Beta Complexed With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine Template Paired with dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: 5'-D(P*GP*TP*CP*GP*G)-3'(Non-covalent)

DG-DT-DC-DG-DG.1:

18 residues within 4Å:

Chain A: C.1, C.2, G.3, A.4, C.5
Chain C: E.26, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Ligands: NA.4

2 PLIP interactions:

2 interactions with chain C

Hydrogen bonds: C:R.283
pi-Stacking: C:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

Chain C: D.190, D.192
Ligands: DCP.5

3 PLIP interactions:

2 interactions with chain C, 1 Ligand-Water interactions

Metal complexes: C:D.190, C:D.192, H₂O.1

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

NA.3:	5 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, I.106 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.103, C:G.105, C:I.106, C:I.106
NA.4:	5 residues within 4Å: Chain C: K.60, K.61, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.61, C:V.65

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.5:

19 residues within 4Å:

Chain A: G.6, G.7
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: MG.2

15 PLIP interactions:

15 interactions with chain C

Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:S.180, C:R.183, C:G.189, C:D.190, C:T.273
Water bridges: C:R.149, C:R.149, C:R.183, C:D.192, C:D.192, C:D.276
Salt bridges: C:R.183

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Krahn, J.M. et al., Structure of DNA Polymerase beta with the Mutagenic DNA Lesion 8-oxodeoxyguanine Reveals Structural Insights into its Coding Potential. Structure (2003)

Release Date

2003-01-28

Peptides

DNA POLYMERASE BETA: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
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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