8vfd.1 | SWISS-MODEL Template Library

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SMTL ID : 8vfd.1

Ternary DNA Polymerase Beta bound to DNA containing template FapydG incoming TTP analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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:

16 residues within 4Å:

Chain A: H.34, K.35, A.38, Y.39, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Chain B: C.1, C.2, G.3, A.4, C.5

1 PLIP interactions:

1 interactions with chain A

pi-Stacking: A:H.34

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

NA.2:

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

1 x 01: 1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione

01.3:

17 residues within 4Å:

Chain A: 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
Chain B: X.6
Chain C: A.10
Ligands: MN.4, MN.5

9 PLIP interactions:

9 interactions with chain A

Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:G.189, A:D.190, A:G.274, A:N.279
Water bridges: A:R.149, A:R.149

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.4:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: 01.3, MN.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.2
MN.5:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: A.10 Ligands: 01.3, MN.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H₂O.1, H₂O.4

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: 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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