6crh.1 | SWISS-MODEL Template Library

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SMTL ID : 6crh.1

Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 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:

19 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, K.72
Chain B: C.1, C.2, G.3, A.4, C.5
Ligands: NA.5

1 PLIP interactions:

1 interactions with chain A

pi-Stacking: A:H.34

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: MG.3, XG4.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, H₂O.2, H₂O.2
MG.3:	5 residues within 4Å: Chain A: D.190, D.192 Chain C: A.10 Ligands: MG.2, XG4.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:D.190, A:D.192, H₂O.1, H₂O.2

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

NA.4:	6 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106
NA.5:	4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.65, A:V.65

1 x XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.6:

18 residues within 4Å:

Chain A: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, G.274, S.275, D.276, N.279
Chain B: X.6, T.7
Chain C: A.10
Ligands: MG.2, MG.3

14 PLIP interactions:

14 interactions with chain A

Hydrogen bonds: A:S.180, A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.190, A:Y.271, A:D.276
Water bridges: A:R.149, A:R.149, A:S.188
Salt bridges: A:D.276

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Kou, Y. et al., Promutagenicity of 8-Chloroguanine, A Major Inflammation-Induced Halogenated DNA Lesion. Molecules (2019)

Release Date

2019-03-20

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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