SMTL ID : 4jwm.1

Ternary complex of D256E mutant of DNA Polymerase Beta

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.280, A:R.283 Water bridges: A:H.34, A:N.37, A:K.280 Salt bridges: A:K.280 pi-Stacking: A:H.34

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 B: A.6 Chain C: C.10 Ligands: MG.3, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:D.276 Hydrogen bonds: A:S.180, A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:N.279 Water bridges: A:R.149, A:R.149, A:R.149, A:S.188, A:R.254, A:R.254, A:D.276, 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.1 MG.4: 6 residues within 4Å: Chain A: D.190, D.192, E.256 Chain C: C.10 Ligands: DUP.2, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.1, H2O.16

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:G.105, A:I.106, 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:V.65, A:V.65 Water bridges: A:K.60

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

CL.7: 4 residues within 4Å: Chain A: N.294, Y.296, T.297, R.299 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: A.32, H.34, K.35 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: E.329, P.330, K.331 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: K.81, L.82, L.85, R.89 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Batra, V.K. et al., Amino Acid Substitution in the Active Site of DNA Polymerase beta Explains the Energy Barrier of the Nucleotidyl Transfer Reaction. J.Am.Chem.Soc. (2013)

Release Date

2013-06-26

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta