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SMTL ID : 5v1r.1

DNA polymerase beta reactant complex with 8-oxoG:C at the primer terminus and incoming dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 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.6

4 PLIP interactions:

4 interactions with chain C

Hydrogen bonds: C:R.283, C:R.283, C:R.283
pi-Stacking: C:H.34

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

MG.2:	3 residues within 4Å: Chain B: C.11 Ligands: DCP.11, PPV.12 No protein-ligand interaction detected (PLIP)
MG.3:	6 residues within 4Å: Chain B: C.11 Chain C: D.190, D.192 Ligands: MG.4, DCP.11, PPV.12 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H₂O.4
MG.4:	7 residues within 4Å: Chain B: G.10, C.11 Chain C: D.190, D.192, D.256 Ligands: MG.3, DCP.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, C:D.256, H₂O.2

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

NA.5:	6 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, G.105, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.103, C:G.105, C:I.106
NA.6:	5 residues within 4Å: Chain C: K.60, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.60, C:V.65

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

CL.7:	5 residues within 4Å: Chain C: D.263, Q.264, Y.266, C.267, V.313 Ligand excluded by PLIP
CL.8:	4 residues within 4Å: Chain C: A.32, I.33, H.34, K.35 Ligand excluded by PLIP
CL.9:	3 residues within 4Å: Chain C: K.81, L.82, E.86 Ligand excluded by PLIP
CL.10:	4 residues within 4Å: Chain C: N.294, Y.296, T.297, R.299 Ligand excluded by PLIP

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.11:

22 residues within 4Å:

Chain A: G.6
Chain B: G.10, C.11
Chain C: R.149, 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
Ligands: MG.2, MG.3, MG.4, PPV.12

14 PLIP interactions:

14 interactions with chain C

Hydrophobic interactions: C:D.276
Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:S.180, C:R.183, C:G.189, C:D.190, C:D.192, C:N.279
Water bridges: C:R.149, C:R.149, C:D.276
Salt bridges: C:R.183

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.12:

11 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, DCP.11

11 PLIP interactions:

11 interactions with chain C

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