5bpc.1 | SWISS-MODEL Template Library

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SMTL ID : 5bpc.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Chain C: C.1, C.2, G.3, A.4, C.5

2 PLIP interactions:

2 interactions with chain A

Water bridges: A:H.34
pi-Stacking: A:H.34

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.2:	5 residues within 4Å: Chain A: D.190, D.192, D.256 Ligands: MN.3, F2A.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H₂O.6, H₂O.6
MN.3:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: MN.2, F2A.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.4
MN.4:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.5:	3 residues within 4Å: Chain A: E.295 Chain C: X.6, G.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.295, H₂O.1

1 x F2A: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine(Non-covalent)

F2A.6:

19 residues within 4Å:

Chain A: 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, K.280
Chain B: C.10
Chain C: X.6
Ligands: MN.2, MN.3

13 PLIP interactions:

13 interactions with chain A

Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:Y.271, A:N.279, A:K.280, A:K.280
Water bridges: A:R.149, A:R.149, A:D.276

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

NA.7:

5 residues within 4Å:

Chain A: T.101, V.103, G.105, I.106
Chain B: G.9

3 PLIP interactions:

3 interactions with chain A

Hydrogen bonds: A:G.105, A:I.106, A:I.106

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: 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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