SMTL ID : 3spz.1

DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA (Ca2+)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.43 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: 18 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, A.415, Y.416, P.417, R.482, K.486, K.560, N.564, T.622, D.623 Chain B: A.2, G.3 Chain C: C.13 Ligands: CA.2, CA.3 9 PLIP interactions: 9 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 Salt bridges: A:R.482, A:K.486, A:K.560

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: UPC.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.411, A:L.412, A:D.623 CA.3: 5 residues within 4Å: Chain A: D.411, D.623, S.624 Chain C: C.13 Ligands: UPC.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.411 CA.4: 3 residues within 4Å: Chain A: N.505, N.507, K.531 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.505, A:K.531, H2O.1, H2O.1 CA.5: 2 residues within 4Å: Chain A: D.114, E.116 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.116, A:E.116

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

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