SMTL ID : 3spy.1

RB69 DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

1 x UPC: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine(Non-covalent)

UPC.1: 17 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, A.415, Y.416, P.417, R.482, K.560, N.564, T.622, D.623 Chain B: A.4, G.5 Chain C: C.13 Ligands: MG.2, MG.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:A.415, A:Y.416, A:N.564, A:N.564 Water bridges: A:D.411, A:L.412, A:K.486, A:K.486, A:Q.556, A:E.686 Salt bridges: A:R.482, A:K.486, A:K.560

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: UPC.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.411, A:L.412, A:D.623 MG.3: 5 residues within 4Å: Chain A: D.411, D.623 Chain C: C.13 Ligands: UPC.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.411, A:D.623, H2O.14, H2O.19 MG.4: 7 residues within 4Å: Chain A: A.502, N.505, P.506, N.507, I.530, K.531, L.533 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.505, A:K.531 MG.5: 2 residues within 4Å: Chain A: K.486, E.716 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: D.114, E.116 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.114, A:E.116, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase. Biochemistry (2011)

Release Date

2011-10-12

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase