3mby.1 | SWISS-MODEL Template Library

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SMTL ID : 3mby.1

Ternary complex of DNA Polymerase BETA with template base A and 8oxodGTP in the active site with a dideoxy terminated primer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: H.34, K.35, A.38, Y.39, L.62, 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
Ligands: NA.6

4 PLIP interactions:

4 interactions with chain A

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

1 x 8DG: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

8DG.2:

18 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, S.275, D.276, N.279
Chain B: A.6
Chain C: C.10
Ligands: MG.3, NA.4

17 PLIP interactions:

17 interactions with chain A

Hydrogen bonds: A:S.180, A:S.180, A:S.180, A:R.183, A:G.189, A:D.190, A:N.279
Water bridges: A:Y.36, A:R.40, A:R.149, A:R.149, A:R.149, A:R.183, A:S.188, A:D.276
Salt bridges: A:R.183, A:D.276

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

4 residues within 4Å:

Chain A: D.190, D.192
Ligands: 8DG.2, NA.4

3 PLIP interactions:

2 interactions with chain A, 1 Ligand-Water interactions

Metal complexes: A:D.190, A:D.192, H₂O.2

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

NA.4:	5 residues within 4Å: Chain A: D.190, D.192, D.256 Ligands: 8DG.2, MG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.190
NA.5:	5 residues within 4Å: Chain A: T.101, V.103, S.104, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106
NA.6:	4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.60, A:G.64, A:V.65

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.7:	4 residues within 4Å: Chain A: A.32, I.33, H.34, K.35 Ligand excluded by PLIP
CL.8:	4 residues within 4Å: Chain A: K.81, L.82, E.86, R.89 Ligand excluded by PLIP
CL.9:	4 residues within 4Å: Chain A: N.294, Y.296, T.297, R.299 Ligand excluded by PLIP

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Batra, V.K. et al., Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-06-09

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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