SMTL ID : 6h1v.1

The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 6 residues within 4Å: Chain A: D.664, C.665, C.677, A.678, C.763, R.765 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.665, A:C.677, A:C.763

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

DTP.2: 17 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, T.876, D.877 Chain B: C.11 Chain C: T.5, G.6 Ligands: MG.3 11 PLIP interactions: 11 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 Salt bridges: A:R.781, A:K.785, A:K.824, A:K.824, A:K.824

1 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ter Beek, J. et al., Structural evidence for an essential Fe-S cluster in the catalytic core domain of DNA polymerase ε. Nucleic Acids Res. (2019)

Release Date

2019-04-24

Peptides

DNA polymerase epsilon catalytic subunit A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase epsilon catalytic subunit A