SMTL ID : 4m8o.1

TERNARY COMPLEX OF DNA POLYMERASE EPSILON WITH AN INCOMING dATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 18 residues within 4Å: Chain A: D.640, V.641, A.642, S.643, M.644, Y.645, P.646, R.781, K.785, K.824, N.828, Y.831, T.876, D.877 Chain B: C.11 Chain C: T.5, G.6 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.645 Hydrogen bonds: A:S.643, A:M.644, A:Y.645, A:N.828 Water bridges: A:Y.431, A:Y.431, A:D.640, A:K.785, A:K.785, A:K.824, A:D.877 Salt bridges: A:R.781, A:R.781, A:K.785, A:K.824, A:K.824, A:K.824

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.640, V.641, D.877 Ligands: DTP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.640, A:V.641, A:D.877

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.665, C.668, C.677, C.763 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.665, A:C.668, A:C.677, A:C.763

2 x TAU: 2-AMINOETHANESULFONIC ACID(Non-covalent)

TAU.4: 2 residues within 4Å: Chain A: K.427, R.428 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.424, A:R.424, A:R.424, A:T.512 Salt bridges: A:K.427 TAU.5: 5 residues within 4Å: Chain A: A.979, E.980, L.981, K.982, K.987 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.981 Water bridges: A:K.987 Salt bridges: A:K.982, A:K.987

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

CL.6: 1 residues within 4Å: Chain B: U.10 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: U.9 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hogg, M. et al., Structural basis for processive DNA synthesis by yeast DNA polymerase epsilon. Nat.Struct.Mol.Biol. (2014)

Release Date

2013-11-27

Peptides

DNA polymerase epsilon catalytic subunit A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase epsilon catalytic subunit A