SMTL ID : 4r65.1

Ternary complex crystal structure of R258A mutant of DNA polymerase Beta

Coordinates

PDB Format

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: 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 B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.6 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:H.34, A:K.230, A:K.230, A:T.233, A:T.233, A:K.234, A:K.234, A:K.234, A:K.234, A:Y.271, A:Y.271, A:R.283, A:T.292, A:N.294, A:Y.296 Salt bridges: A:K.280 Water bridges: A:H.34, A:N.133, A:H.134, A:S.229, A:K.280, A:I.293

1 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.2: 18 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 Chain C: C.10 Chain B: A.6 Ligands: MG.3, MG.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:D.276 Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.192, A:N.279 Water bridges: A:R.149, A:S.180, A:D.190, A:D.276

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: DUP.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.2728 MG.4: 6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: C.10 Ligands: DUP.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H2O.2729

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

NA.5: 6 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106 NA.6: 4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.62, A:V.65 Water bridges: A:K.60

6 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: 4 residues within 4Å: Chain A: A.32, I.33, H.34, K.35 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: Q.159, T.176, V.177 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: N.294, Y.296, T.297, R.299 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: K.81, L.82, L.85, R.89 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: F.25, K.84 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Beard, W.A. et al., Substrate-induced DNA Polymerase beta Activation. J.Biol.Chem. (2014)

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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