4ub4.1 | SWISS-MODEL Template Library

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SMTL ID : 4ub4.1

DNA polymerase beta substrate complex with a templating cytosine and incoming dGTP, 0 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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:

17 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 C: C.1, C.2, G.3, A.4, C.5

3 PLIP interactions:

3 interactions with chain A

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

2 x CA: CALCIUM ION(Non-covalent)

CA.2:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain B: C.10 Ligands: CA.3, DGT.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.190, A:D.192, A:D.256, H₂O.8
CA.3:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: CA.2, DGT.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.190, A:D.192, H₂O.2

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.4:

21 residues within 4Å:

Chain A: 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
Chain B: C.10
Chain C: C.6, G.7
Ligands: CA.2, CA.3

15 PLIP interactions:

15 interactions with chain A

Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:S.180, A:R.183, A:G.189, A:D.190, A:D.190, A:N.279, A:R.283
Water bridges: A:F.181, A:F.181, A:R.183, A:D.276
Salt bridges: A:R.183

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: 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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Transparent

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