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SMTL ID : 6cub.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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:

19 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, K.72
Chain B: C.1, C.2, G.3, A.4, C.5
Ligands: NA.6

1 PLIP interactions:

1 interactions with chain A

pi-Stacking: A:H.34

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

DZ4.2:

18 residues within 4Å:

Chain A: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, G.274, S.275, D.276, N.279, K.280
Chain B: X.6
Chain C: A.10
Ligands: MN.3, MN.4

11 PLIP interactions:

11 interactions with chain A

Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.276, A:N.279, A:K.280
Water bridges: A:D.190, A:D.276

2 x MN: MANGANESE (II) ION(Non-covalent)

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

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

NA.5:	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.6:	4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.60, A:V.65

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

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

Release Date

2019-03-27

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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