SMTL ID : 6cr3.1

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:K.280 Hydrogen bonds: C:R.283 Water bridges: C:H.34, C:H.34, C:N.37, C:K.280, C:K.280 Salt bridges: C:K.280 pi-Stacking: C:H.34

1 x H84: 2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine(Non-covalent)

H84.2: 19 residues within 4Å: Chain A: T.6, G.7 Chain B: C.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 Ligands: MG.3, NA.6 14 PLIP interactions: 14 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 Water bridges: C:R.149, C:R.149, C:D.190, C:D.276, C:D.276, C:D.276

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain C: D.190, D.192 Ligands: H84.2, NA.6 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H2O.7

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

NA.4: 5 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, 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, K.61, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.60, C:V.65 Water bridges: C:K.60 NA.6: 6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: H84.2, MG.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.256

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

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

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

2018-06-27

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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