SMTL ID : 3v7k.1

Co-crystal structure of K72E variant of rat polymerase beta: Enzyme-DNA binary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

1 x DA- DT- DG- DT- DG- DA- DG- DT: DNA (5'-D(P*AP*TP*GP*TP*GP*AP*GP*T)-3')(Non-covalent)

DA-DT-DG-DT-DG-DA-DG-DT.1: 20 residues within 4Å: Chain A: V.108, T.109, G.110, I.111, G.112, P.113, S.114, A.115, M.241, R.259, D.261 Chain B: A.3, A.4, C.5, T.6, C.7, A.8, C.9, A.10 Ligands: NA.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.235, A:K.235, A:G.236, A:T.238, A:T.238, A:K.239, A:Y.276, A:Y.276, A:N.284, A:R.288, A:R.288, A:Y.301 Water bridges: A:H.139, A:H.140, A:E.237, A:E.237 Salt bridges: A:R.45

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

NA.2: 1 residues within 4Å: Chain A: D.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.195 NA.3: 1 residues within 4Å: Chain A: D.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.195 NA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.5: 4 residues within 4Å: Chain A: T.106, I.111 Ligands: DA-DT-DG-DT-DG-DA-DG-DT.1, DA-DT-DG-DT-DG-DA-DG-DT.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rangarajan, S. et al., Crystallographic studies of K72E mutant DNA polymerase explain loss of lyase function and reveal changes in the overall conformational state of the polymerase domain. To be Published

Release Date

2013-01-16

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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