5v1n.1 | SWISS-MODEL Template Library

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SMTL ID : 5v1n.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 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

8 PLIP interactions:

8 interactions with chain C

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

2 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2:	3 residues within 4Å: Chain C: D.190, D.192 Ligands: DCP.7 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H₂O.5
CA.3:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.4:

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:G.105, C:I.106, C:I.106

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

CL.5:	2 residues within 4Å: Chain C: K.81, L.82 Ligand excluded by PLIP
CL.6:	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.7:

18 residues within 4Å:

Chain A: G.6
Chain B: G.10
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: CA.2

17 PLIP interactions:

17 interactions with chain C

Hydrophobic interactions: C:D.276
Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:R.183, C:G.189, C:D.190, C:D.192, C:N.279
Water bridges: C:F.181, C:F.181, C:R.183, C:R.183, C:D.276, C:D.276, C:D.276
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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