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SMTL ID : 8vfb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 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: C.1, C.2, G.3, A.4, C.5
Chain C: H.34, K.35, A.38, Y.39, L.62, G.64, V.65, G.66, T.67, K.68, I.69

2 PLIP interactions:

2 interactions with chain C

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

1 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.2:

21 residues within 4Å:

Chain A: C.6, X.7
Chain B: A.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, R.283
Ligands: MN.4, MN.5

9 PLIP interactions:

9 interactions with chain C

Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:N.279, C:R.283

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

NA.3:

5 residues within 4Å:

Chain B: G.9
Chain C: T.101, V.103, S.104, I.106

3 PLIP interactions:

3 interactions with chain C

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

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

MN.4:	4 residues within 4Å: Chain C: S.180, D.190, D.192 Ligands: G2P.2 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.190, C:D.192, C:D.192
MN.5:	5 residues within 4Å: Chain B: A.10 Chain C: D.190, D.192, D.256 Ligands: G2P.2 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.190, C:D.192, C:D.256

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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