6e3v.1 | SWISS-MODEL Template Library

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SMTL ID : 6e3v.1

Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable TTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 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: K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69, K.72
Chain B: C.1, C.2, G.3, A.4, C.5
Ligands: NA.5

2 PLIP interactions:

2 interactions with chain A

Hydrogen bonds: A:R.283
pi-Stacking: A:H.34

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: MG.3, 1FZ.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.2
MG.3:	5 residues within 4Å: Chain A: D.190, D.192, D.256 Ligands: MG.2, 1FZ.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.190, A:D.192, H₂O.5

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

NA.4:	4 residues within 4Å: Chain A: T.101, V.103, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106
NA.5:	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:L.62, A:G.64, A:V.65

1 x 1FZ: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine(Non-covalent)

1FZ.6:

19 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
Chain B: A.6
Chain C: A.10
Ligands: MG.2, MG.3

14 PLIP interactions:

14 interactions with chain A

Hydrophobic interactions: A:D.276
Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.192, A:D.192, A:N.279
Water bridges: A:R.149, A:S.188, A:D.276

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Koag, M.C. et al., Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases. J. Am. Chem. Soc. (2019)

Release Date

2019-04-03

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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