7s9q.1 | SWISS-MODEL Template Library

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SMTL ID : 7s9q.1

Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dATP analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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:

19 residues within 4Å:

Chain A: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69, K.72
Chain C: C.1, C.2, G.3, A.4, C.5
Ligands: NA.6

1 PLIP interactions:

1 interactions with chain A

pi-Stacking: A:H.34

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

NA.2:	5 residues within 4Å: Chain A: T.101, V.103, S.104, I.106 Chain B: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106
NA.3:	4 residues within 4Å: Chain A: A.32, I.33, H.34, K.35 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.32, A:H.34, A:K.35 Water bridges: A:I.33
NA.6:	4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.65, A:V.65

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

MN.4:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain B: A.10 Ligands: MN.5, F2A.7 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.14
MN.5:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: MN.4, F2A.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.3
MN.8:	2 residues within 4Å: Chain A: T.121, D.124 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.124, H₂O.4, H₂O.6, H₂O.6, H₂O.7

1 x F2A: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine(Non-covalent)

F2A.7:

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

13 PLIP interactions:

13 interactions with chain A

Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:Y.271, A:D.276
Water bridges: A:R.149, A:R.149, A:R.149, A:D.276, A:E.295

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9:	1 residues within 4Å: Chain A: H.51 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.51, H₂O.6, H₂O.11, H₂O.11, H₂O.13
MG.10:	3 residues within 4Å: Chain A: Q.240, E.249, H.252 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.252, H₂O.4, H₂O.7, H₂O.10

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Ryan, B.J. et al., Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J.Am.Chem.Soc. (2022)

Release Date

2022-08-03

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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