SMTL ID : 6nkr.1

Ternary complex crystal structure of K289M variant of DNA polymerase Beta with dGTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 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: 17 residues within 4Å: Chain A: K.35, A.38, Y.39, P.63, G.64, V.65, G.66, T.67, K.68, I.69, E.288 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: NA.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.280 Hydrogen bonds: A:R.283 Salt bridges: A:K.280 pi-Stacking: A:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: NA.3, DGT.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.1

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

NA.3: 6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain B: C.10 Ligands: MG.2, DGT.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192 NA.4: 6 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, I.106 Chain B: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106 NA.5: 5 residues within 4Å: Chain A: K.60, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.60, A:G.64, A:V.65

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: N.294, T.297, R.299 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: D.263, Q.264, Y.266, C.267, V.313 Ligand excluded by PLIP

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.8: 20 residues within 4Å: Chain A: 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 Chain B: C.10 Chain C: C.6, G.7 Ligands: MG.2, NA.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.180, A:S.180, A:S.180, A:R.183, A:G.189, A:D.190, A:D.190, A:D.190, A:N.279, A:R.283 Water bridges: A:R.149, A:R.149, A:D.276 Salt bridges: A:R.183

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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