7s9p.1 | SWISS-MODEL Template Library

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SMTL ID : 7s9p.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 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:

18 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
Ligands: NA.6

3 PLIP interactions:

3 interactions with chain C

Hydrogen bonds: C:K.280, C:R.283
pi-Stacking: C:H.34

1 x XC5: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine(Non-covalent)

XC5.2:

18 residues within 4Å:

Chain A: X.6
Chain B: A.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, S.275, D.276, N.279
Ligands: MN.3, MN.4

19 PLIP interactions:

19 interactions with chain C

Hydrophobic interactions: C:D.276
Hydrogen bonds: C:S.180, C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:N.279
Water bridges: C:R.149, C:R.149, C:R.149, C:R.149, C:S.188, C:D.190, C:D.190, C:D.276, C:D.276, C:D.276

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

MN.3:	4 residues within 4Å: Chain C: D.190, D.192 Ligands: XC5.2, MN.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H₂O.6
MN.4:	6 residues within 4Å: Chain B: A.10 Chain C: D.190, D.192, D.256 Ligands: XC5.2, MN.3 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, C:D.256, H₂O.6
MN.5:	2 residues within 4Å: Chain C: D.145, H.252 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.145, C:H.252, H₂O.10, H₂O.15

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

NA.6:	4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.60, C:V.65
NA.7:	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.8:	4 residues within 4Å: Chain C: A.32, I.33, H.34, K.35 Ligand excluded by PLIP
CL.9:	2 residues within 4Å: Chain C: N.294, T.297 Ligand excluded by PLIP

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: 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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