SMTL ID : 6nks.1

Ternary complex crystal structure of K289M variant of DNA polymerase Beta with beta-gamma CHF analog of dGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 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: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: NA.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.280 Hydrogen bonds: A:R.283 Water bridges: A:N.37 Salt bridges: A:K.280 pi-Stacking: A:H.34

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

GFH.2: 21 residues within 4Å: Chain A: R.149, 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.3, NA.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.149, A:R.149, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.190, A:D.192, A:N.279, A:R.283 Water bridges: A:D.276 Halogen bonds: A:R.183

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: GFH.2, NA.4 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.4: 6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain B: C.10 Ligands: GFH.2, MG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.256 NA.5: 5 residues within 4Å: Chain A: T.101, V.103, S.104, I.106 Chain B: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106 NA.6: 6 residues within 4Å: Chain A: K.60, K.61, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.62

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

CL.7: 3 residues within 4Å: Chain A: E.329, P.330, K.331 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: N.294, T.297, R.299 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: A.32, I.33, H.34, K.35 Ligand excluded by PLIP

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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