5bol.1 | SWISS-MODEL Template Library

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SMTL ID : 5bol.1

DNA polymerase beta ternary complex with a templating 5ClC and incoming dGTP analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 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:

17 residues within 4Å:

Chain A: 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

4 PLIP interactions:

4 interactions with chain C

Hydrogen bonds: C:R.283
Water bridges: C:H.34, C:K.280
pi-Stacking: C:H.34

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2:	6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: MG.4, 1GC.5 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, C:D.256, H₂O.3
MG.4:	4 residues within 4Å: Chain C: D.190, D.192 Ligands: MG.2, 1GC.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H₂O.4

1 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

3 PLIP interactions:

3 interactions with chain C

Hydrogen bonds: C:V.103, C:G.105, C:I.106

1 x 1GC: 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine(Non-covalent)

1GC.5:

20 residues within 4Å:

Chain A: X.6, G.7
Chain B: C.10
Chain C: 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, R.283
Ligands: MG.2, MG.4

16 PLIP interactions:

16 interactions with chain C

Hydrogen bonds: C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:N.279, C:R.283
Water bridges: C:R.40, C:R.149, C:R.149, C:D.190, C:D.190, C:D.276, C:D.276, C:D.276

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Fedeles, B.I. et al., Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-08-19

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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