5v1o.1 | SWISS-MODEL Template Library

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SMTL ID : 5v1o.1

DNA polymerase beta product complex with 8-oxoG:A and inserted dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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:

18 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
Ligands: NA.5

8 PLIP interactions:

8 interactions with chain C

Hydrogen bonds: C:N.279, C:K.280, C:R.283, C:R.283, C:R.283
Water bridges: C:N.37
Salt bridges: C:K.280
pi-Stacking: C:H.34

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2:	2 residues within 4Å: Chain B: C.11 Ligands: PPV.10 No protein-ligand interaction detected (PLIP)
MG.3:	5 residues within 4Å: Chain B: C.11 Chain C: D.190, D.192 Ligands: NA.9, PPV.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H₂O.5

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

NA.4:	4 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.103, C:G.105, C:I.106
NA.5:	4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.62, C:V.65
NA.9:	6 residues within 4Å: Chain B: G.10, C.11 Chain C: D.190, D.192, D.256 Ligands: MG.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.190

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

CL.6:	5 residues within 4Å: Chain C: D.263, Q.264, Y.266, C.267, V.313 Ligand excluded by PLIP
CL.7:	3 residues within 4Å: Chain C: K.81, L.82, R.89 Ligand excluded by PLIP
CL.8:	4 residues within 4Å: Chain C: N.294, Y.296, T.297, R.299 Ligand excluded by PLIP

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.10:

10 residues within 4Å:

Chain B: C.11
Chain C: G.179, S.180, R.183, S.188, G.189, D.190, D.192
Ligands: MG.2, MG.3

9 PLIP interactions:

9 interactions with chain C

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Whitaker, A.M. et al., Capturing a mammalian DNA polymerase extending from an oxidized nucleotide. Nucleic Acids Res. (2017)

Release Date

2017-05-10

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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