SMTL ID : 3scx.1

RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the Presence of Ca2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

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

DUP.1: 18 residues within 4Å: Chain A: A.4, G.5 Chain B: C.13 Chain C: D.411, L.412, S.414, L.415, Y.416, P.417, R.482, K.486, K.560, N.564, T.622, D.623 Ligands: CA.3, CA.4, CA.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.416 Hydrogen bonds: C:S.414, C:L.415, C:Y.416, C:N.564 Water bridges: C:R.482, C:K.486, C:K.486, C:K.486, C:K.560 Salt bridges: C:R.482, C:K.486, C:K.560

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain C: N.505, N.507, K.531 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:N.505, C:K.531 CA.3: 5 residues within 4Å: Chain C: D.411, L.412, S.414, D.623 Ligands: DUP.1 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.411, C:D.411, C:L.412, C:D.623 CA.4: 4 residues within 4Å: Chain B: C.13 Chain C: D.411, D.623 Ligands: DUP.1 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.411, C:D.623 CA.5: 3 residues within 4Å: Chain C: R.482, K.486 Ligands: DUP.1 No protein-ligand interaction detected (PLIP)

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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