SMTL ID : 3s9h.1

RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) ternary complex with dUpNpp and a dideoxy-terminated primer in the presence of Ca2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

7 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.3: 5 residues within 4Å: Chain C: D.411, L.412, D.623 Ligands: DUP.2, CA.4 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.411, C:D.411, C:L.412, C:D.623, H2O.6 CA.4: 6 residues within 4Å: Chain B: C.13 Chain C: D.411, D.623, S.624 Ligands: DUP.2, CA.3 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.411, C:D.623, H2O.6, H2O.6 CA.5: 4 residues within 4Å: Chain C: R.482, K.486, K.560 Ligands: DUP.2 No protein-ligand interaction detected (PLIP) CA.6: 1 residues within 4Å: Chain C: E.116 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.116, C:E.116, H2O.7, H2O.7, H2O.7 CA.7: 3 residues within 4Å: Chain C: N.505, N.507, K.531 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:N.505, C:K.531, H2O.7, H2O.7, H2O.7 CA.8: 2 residues within 4Å: Chain C: Q.481, R.559 No protein-ligand interaction detected (PLIP)

1 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.2: 18 residues within 4Å: Chain A: A.4, G.5 Chain B: C.13 Chain C: D.411, L.412, T.413, S.414, L.415, Y.416, P.417, R.482, K.560, N.564, T.622, D.623 Ligands: CA.3, CA.4, CA.5 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.416 Hydrogen bonds: C:S.414, C:L.415, C:Y.416, C:K.560, C:N.564, C:N.564, C:D.623, C:D.623 Water bridges: C:R.482, C:K.486 Salt bridges: C:R.482, C:K.486, C:K.560

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: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase

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