SMTL ID : 4z6c.1

Structure of human DNA polymerase beta 279NA mutant complexed with G in the template base paired with incoming non-hydrolyzable CTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 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: 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 Ligands: NA.4 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.283, C:R.283, C:R.283 Salt bridges: C:K.280 pi-Stacking: C:H.34

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain B: A.10 Chain C: D.190, D.192, D.256 Ligands: MG.5, 0KX.6 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.190, C:D.190, C:D.192, C:D.256 MG.5: 4 residues within 4Å: Chain C: D.190, D.192 Ligands: MG.2, 0KX.6 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H2O.1

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

NA.3: 4 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, I.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.103 NA.4: 4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.65 Water bridges: C:K.60

1 x 0KX: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine(Non-covalent)

0KX.6: 17 residues within 4Å: Chain A: G.6 Chain B: A.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, D.276, A.279 Ligands: MG.2, MG.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:D.276 Hydrogen bonds: C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.C. et al., Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase beta. Biochem. J. (2018)

Release Date

2016-04-13

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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