SMTL ID : 3v7j.1

Co-crystal structure of Wild Type Rat polymerase beta: Enzyme-DNA binary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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: 22 residues within 4Å: Chain A: V.108, T.109, G.110, I.111, G.112, P.113, S.114, A.115, H.140, M.241, R.259, D.261 Chain B: A.3, A.4, C.5, T.6, C.7, A.8, C.9, A.10, T.11 Ligands: NA.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:D.281 Hydrogen bonds: A:K.235, A:K.235, A:G.236, A:T.238, A:K.239, A:K.239, A:Y.276, A:N.284, A:R.288 Water bridges: A:H.139, A:H.140, A:H.140, A:E.237, A:E.237, A:T.238 Salt bridges: A:R.45

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

NA.2: 4 residues within 4Å: Chain A: C.183, G.184, D.195, D.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.195, A:D.197 Water bridges: A:S.185, A:F.186 NA.3: 2 residues within 4Å: Chain A: K.132, D.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.132 Water bridges: A:D.135 NA.4: 5 residues within 4Å: Chain A: T.106, R.107, V.108, T.109 Ligands: DA-DT-DG-DT-DG-DA-DG-DT.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.106 NA.5: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.65, A:K.65 NA.6: 3 residues within 4Å: Chain A: Y.44, K.73, K.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.44, A:K.77, A:K.77 NA.7: 1 residues within 4Å: Chain A: A.43 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.46, A:K.46 NA.8: 6 residues within 4Å: Chain A: N.33, V.34, Q.36, I.102, P.113, R.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.36 NA.9: 5 residues within 4Å: Chain A: S.234, K.239, F.240, M.241 Chain B: C.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.239

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

CL.10: 4 residues within 4Å: Chain A: L.275, T.278, G.279, R.338 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain A: R.157, M.160, F.186, A.190, S.192, S.193 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: E.122 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: L.137, N.138 Ligand excluded by PLIP

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