SMTL ID : 6nkz.1

Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma methylene dGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x DT- DT- DC- DG- DG: DNA (5'-D(P*TP*TP*CP*GP*G)-3')(Non-covalent)

DT-DT-DC-DG-DG.1: 17 residues within 4Å: Chain A: C.1, C.2, G.3, A.4, A.5 Chain C: K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69 Ligands: NA.3 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:K.280 Hydrogen bonds: C:R.283 Water bridges: C:H.34, C:K.280, C:K.280 Salt bridges: C:K.280 pi-Cation interactions: C:H.34

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

NA.2: 5 residues within 4Å: Chain B: T.9 Chain C: T.101, V.103, S.104, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.103, C:G.105, C:I.106 NA.3: 5 residues within 4Å: Chain C: K.60, L.62, P.63, V.65 Ligands: DT-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.62, C:V.65 Water bridges: C:K.60 NA.5: 6 residues within 4Å: Chain B: T.10 Chain C: D.190, D.192, D.256 Ligands: MG.4, GGH.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.256

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x GGH: 2'-DEOXY-5'-O-(HYDROXY{[HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]OXY}PHOSPHORYL)GUANOSINE(Non-covalent)

GGH.6: 20 residues within 4Å: Chain A: C.6, A.7 Chain B: T.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: MG.4, NA.5 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:D.192, C:N.279, C:R.283 Water bridges: C:R.149, C:R.149, C:D.190, C:D.276, C:D.276, C:D.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Batra, V.K. et al., Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography. Biochemistry (2020)

Release Date

2020-01-08

Peptides

DNA Polymerase Beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA Polymerase Beta

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