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SMTL ID : 2i9g.1

DNA Polymerase Beta with a Benzo[c]phenanthrene diol epoxide adducted guanine base

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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 B: C.1, C.2, G.3, A.4, C.5
Chain C: H.34, 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

3 PLIP interactions:

3 interactions with chain C

Water bridges: C:H.34, C:N.37
pi-Stacking: C:H.34

1 x BPI: (1S)-1,2,3,4-TETRAHYDRO-BENZO[C]PHENANTHRENE-2,3,4-TRIOL(Non-covalent)

BPI.2:

6 residues within 4Å:

Chain A: C.10
Chain B: G.6, G.7
Chain C: N.37, R.40, Y.271

2 PLIP interactions:

2 interactions with chain C

Hydrogen bonds: C:N.37, C:R.40

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

NA.3:	5 residues within 4Å: Chain A: G.9 Chain C: T.101, V.103, S.104, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.103, C:G.105, C:I.106
NA.4:	5 residues within 4Å: Chain C: K.60, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.60, C:G.64, C:V.65

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

CL.5:	3 residues within 4Å: Chain C: N.294, T.297, R.299 Ligand excluded by PLIP
CL.6:	1 residues within 4Å: Chain C: T.93 Ligand excluded by PLIP

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Batra, V.K. et al., Structure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-10-24

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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