SMTL ID : 7r3x.1

The crystal structure of the L439V variant of Pol2CORE in complex with DNA and an incoming nucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

monomer

Ligands

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

DTP.1: 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, Y.831, D.877 Chain B: C.11 Chain C: T.5, G.6 Ligands: CA.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.645 Hydrogen bonds: A:V.641, A:S.643, A:M.644, A:Y.645, A:N.828 Salt bridges: A:R.781, A:R.781, A:K.785, A:K.824, A:K.824, A:K.824

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.640, V.641, D.877 Ligands: DTP.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.640, A:D.640, A:V.641, A:D.877 CA.3: 4 residues within 4Å: Chain A: D.290, E.292, D.477 Ligands: ACT.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.290, A:E.292, A:D.477, H2O.1, H2O.2

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

ACT.4: 5 residues within 4Å: Chain A: D.290, F.377, V.439, D.477 Ligands: CA.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.377, A:V.439 Water bridges: A:D.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barbari, S.R. et al., Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ε variants at low dNTP levels. Nucleic Acids Res. (2022)

Release Date

2022-07-27

Peptides

DNA polymerase epsilon catalytic subunit A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase epsilon catalytic subunit A