SMTL ID : 4r66.1

Ternary complex crystal structure of E295K mutant of DNA polymerase Beta

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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: 19 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, MN.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.34 pi-Stacking: A:H.34

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

DUP.2: 19 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 Chain B: A.6 Chain C: C.10 Ligands: MN.3, MN.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.276 Water bridges: A:D.276, A:D.276 Salt bridges: A:R.149

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.3: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: DUP.2, MN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.2 MN.4: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: DUP.2, MN.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.190, A:D.192 MN.10: 2 residues within 4Å: Chain B: A.14, G.15 No protein-ligand interaction detected (PLIP) MN.11: 1 residues within 4Å: Ligands: DG-DT-DC-DG-DG.1 No protein-ligand interaction detected (PLIP)

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.62, A:V.65

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

CL.7: 3 residues within 4Å: Chain A: N.294, T.297, R.299 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: K.81, L.82, R.89 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

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

Release Date

2014-10-08

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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