4ubc.1 | SWISS-MODEL Template Library

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SMTL ID : 4ubc.1

DNA polymerase beta substrate complex with a templating cytosine and incoming 8-oxodGTP, 0 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 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

6 PLIP interactions:

6 interactions with chain C

Hydrophobic interactions: C:K.280
Hydrogen bonds: C:R.283
Water bridges: C:N.37, C:R.40
Salt bridges: C:K.280
pi-Stacking: C:H.34

3 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.2:	1 residues within 4Å: Ligands: 8DG.3 No protein-ligand interaction detected (PLIP)
CA.4:	6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: 8DG.3, CA.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.190, C:D.192, C:D.256, H₂O.6
CA.5:	4 residues within 4Å: Chain C: D.190, D.192 Ligands: 8DG.3, CA.4 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.190, C:D.192, H₂O.6

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

8DG.3:

21 residues within 4Å:

Chain A: C.6, G.7
Chain B: C.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, R.283
Ligands: CA.2, CA.4, CA.5

19 PLIP interactions:

19 interactions with chain C

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