SMTL ID : 6cto.1

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dTTP analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 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.3 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.34, C:K.280, C:R.283 Salt bridges: C:K.280

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

NA.2: 6 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, G.105, 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: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.62, C:G.64, C:V.65 NA.5: 6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: MG.4, VT7.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.192

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain C: D.190, D.192 Ligands: NA.5, VT7.8 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H2O.5

2 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: 6 residues within 4Å: Chain C: D.263, Q.264, Y.265, Y.266, C.267, V.313 Ligand excluded by PLIP

1 x VT7: 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine(Non-covalent)

VT7.8: 19 residues within 4Å: Chain A: A.6 Chain B: C.10 Chain C: 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 Ligands: MG.4, NA.5 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:D.276 Hydrogen bonds: C:R.149, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:D.192, C:N.279 Water bridges: C:S.180, C:D.192, 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., Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry (2018)

Release Date

2018-06-20

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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