4uay.1 | SWISS-MODEL Template Library

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SMTL ID : 4uay.1

DNA polymerase beta product complex with a templating adenine and inserted 8-oxodGMP, 40 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: 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.7

5 PLIP interactions:

5 interactions with chain C

Hydrogen bonds: C:K.280, C:R.283
Water bridges: C:N.37
Salt bridges: C:K.280
pi-Stacking: C:H.34

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2:	2 residues within 4Å: Chain B: G.11 Ligands: PPV.3 No protein-ligand interaction detected (PLIP)
MG.4:	5 residues within 4Å: Chain B: G.11 Chain C: D.190, D.192 Ligands: PPV.3, NA.5 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H₂O.5, H₂O.11

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3:

11 residues within 4Å:

Chain B: G.11
Chain C: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192
Ligands: MG.2, MG.4

10 PLIP interactions:

10 interactions with chain C

Hydrogen bonds: C:S.180, C:S.180, C:G.189, C:D.190
Water bridges: C:R.149, C:S.180, C:D.190, C:D.190
Salt bridges: C:R.149, C:R.183

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

NA.5:	6 residues within 4Å: Chain B: C.10, G.11 Chain C: D.190, D.192, D.256 Ligands: MG.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.190
NA.6:	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:G.105, C:I.106, C:I.106
NA.7:	5 residues within 4Å: Chain C: K.60, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.60, C:V.65 Water bridges: C:K.60

1 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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Freudenthal, B.D. et al., Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature (2015)

Release Date

2014-11-12

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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