SMTL ID : 3cfr.1

Structure of the replicating complex of a POL Alpha family DNA Polymerase, ternary complex 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain C: D.411, L.412, D.623 Ligands: CA.2, TTP.7 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.411, C:L.412, C:D.623, H2O.6 CA.2: 6 residues within 4Å: Chain B: C.13 Chain C: D.411, D.623, S.624 Ligands: CA.1, TTP.7 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.411, C:D.623, H2O.6 CA.3: 5 residues within 4Å: Chain C: D.411, K.486, E.686, E.716 Ligands: TTP.7 No protein-ligand interaction detected (PLIP) CA.4: 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.5: 3 residues within 4Å: Chain C: C.671, E.672, N.676 No protein-ligand interaction detected (PLIP)

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

CL.6: 3 residues within 4Å: Chain C: T.413, R.482, K.483 Ligand excluded by PLIP

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.7: 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, R.482, K.486, K.560, N.564, T.622, D.623 Ligands: CA.1, CA.2, CA.3 11 PLIP interactions: 11 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 Salt bridges: C:R.482, C:K.486, C:K.560, C:K.560, C:K.560

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klimenko, D. et al., Insights into base selectivity from the structures of an RB69 DNA Polymerase triple mutant. To be Published

Release Date

2009-03-10

Peptides

DNA polymerase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase

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