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SMTL ID : 6e3x.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 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.2

1 PLIP interactions:

1 interactions with chain A

pi-Stacking: A:H.34

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

NA.2:	4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.65
NA.3:	6 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: MG.5, DZ4.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.1
MG.5:	5 residues within 4Å: Chain A: D.190, D.192 Chain C: A.10 Ligands: MG.4, DZ4.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.190, A:D.192

1 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.6:

18 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, D.276, N.279
Chain B: A.6
Chain C: A.10
Ligands: MG.4, MG.5

12 PLIP interactions:

12 interactions with chain A

Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.190, A:D.192, A:Y.271, A:N.279

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Koag, M.-C. et al., Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP. To Be Published

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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