SMTL ID : 6qib.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

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

SF4.1: 7 residues within 4Å: Chain A: C.670, C.673, F.675, C.682, A.683, C.768, R.770 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.670, A:C.673, A:C.682, A:C.768

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

DTP.2: 17 residues within 4Å: Chain A: D.645, V.646, A.647, S.648, M.649, Y.650, P.651, R.786, K.790, K.829, N.833, Y.836, D.882 Chain B: C.11 Chain C: T.5, G.6 Ligands: CA.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.650 Hydrogen bonds: A:S.648, A:M.649, A:Y.650, A:N.833 Salt bridges: A:R.786, A:K.790, A:K.829, A:K.829, A:K.829

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.645, V.646, D.882 Ligands: DTP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.645, A:V.646, A:D.882

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

2019-04-17

Peptides

DNA polymerase epsilon catalytic subunit A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase epsilon catalytic subunit A