SMTL ID : 6nky.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 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: 18 residues within 4Å: Chain A: C.1, C.2, G.3, A.4, A.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.5 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.280 Hydrogen bonds: C:R.283 Salt bridges: C:K.280 pi-Stacking: C:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain C: D.190, D.192 Ligands: NA.3, GFH.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.190, C:D.192

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

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

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

CL.6: 4 residues within 4Å: Chain C: A.32, I.33, H.34, K.35 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain C: K.81, L.82, L.85, R.89 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain C: N.294, Y.296, T.297, R.299 Ligand excluded by PLIP

1 x GFH: 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE(Non-covalent)

GFH.9: 19 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, D.276, N.279, R.283 Ligands: MG.2, NA.3 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.276, C:D.276, C:D.276 Halogen bonds: C: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: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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