SMTL ID : 3iay.1

Ternary complex of DNA polymerase delta

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

5 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: 6 residues within 4Å: Chain C: D.542, F.543, D.698 Ligands: DCP.2, CA.4, CA.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.542, C:F.543, C:D.698 CA.4: 5 residues within 4Å: Chain A: C.12 Chain C: D.542, D.698 Ligands: DCP.2, CA.3 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.698, H2O.9, H2O.17 CA.5: 4 residues within 4Å: Chain C: D.542, E.736 Ligands: DCP.2, CA.3 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.542, C:D.542, H2O.17, H2O.17, H2O.21 CA.6: 1 residues within 4Å: Chain C: D.255 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.255, H2O.17, H2O.17, H2O.17, H2O.18

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.2: 19 residues within 4Å: Chain A: C.12 Chain B: G.4, G.5 Chain C: D.542, F.543, N.544, S.545, L.546, Y.547, P.548, R.608, K.635, N.639, Y.642, T.697, D.698 Ligands: CA.3, CA.4, CA.5 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Y.547 Hydrogen bonds: C:S.545, C:S.545, C:L.546, C:Y.547, C:N.639, C:N.639, C:D.698 Water bridges: C:R.608, C:R.608, C:K.612, C:K.612, C:K.635, C:K.635, C:E.736 Salt bridges: C:R.608, C:K.635, C:K.635, C:K.635

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 2 residues within 4Å: Chain C: Q.520, E.522 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.522 Water bridges: C:Q.520 ACT.8: 2 residues within 4Å: Chain C: E.119, H.123 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.119 Water bridges: C:H.123 Salt bridges: C:H.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swan, M.K. et al., Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta. Nat.Struct.Mol.Biol. (2009)

Release Date

2009-09-22

Peptides

DNA polymerase delta catalytic subunit: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase delta catalytic subunit