8vfh.1 | SWISS-MODEL Template Library

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SMTL ID : 8vfh.1

Ternary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dC

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

9 PLIP interactions:

9 interactions with chain C

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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2:	4 residues within 4Å: Chain C: D.190, D.192 Ligands: MG.3, DCP.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H₂O.5
MG.3:	5 residues within 4Å: Chain C: D.190, D.192, D.256 Ligands: MG.2, DCP.5 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, C:D.256, H₂O.3, H₂O.6

1 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

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

DCP.5:

17 residues within 4Å:

Chain A: G.6
Chain B: X.10
Chain C: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, D.276, N.279
Ligands: MG.2, MG.3

15 PLIP interactions:

15 interactions with chain C

Hydrophobic interactions: C:D.276
Hydrogen bonds: 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.183, C:R.183, C:S.188, C:D.276
Salt bridges: C:R.183

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Gao, S. et al., Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta. Nucleic Acids Res. (2024)

Release Date

2024-05-08

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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