SMTL ID : 8b67.1

The crystal structure of M644G variant of DNA Pol Epsilon containing CTP in the polymerase active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.645, V.646, D.882 Ligands: CTP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.645, A:V.646, A:D.882 CA.2: 3 residues within 4Å: Chain A: D.645, E.950 Ligands: CTP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.645, A:E.950 CA.3: 5 residues within 4Å: Chain A: D.295, I.296, E.297, D.482 Ligands: ACT.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.295, A:D.295, A:E.297, A:D.482, ACT.5

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.4: 20 residues within 4Å: Chain A: Y.436, D.645, V.646, A.647, S.648, G.649, Y.650, P.651, R.786, K.829, N.833, Y.836, T.881, D.882, E.950 Chain B: C.11 Chain C: G.5, G.6 Ligands: CA.1, CA.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.436, A:Y.436, A:S.648, A:G.649, A:Y.650, A:N.833 Salt bridges: A:R.786, A:R.786, A:K.829, A:K.829, A:K.829

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

ACT.5: 5 residues within 4Å: Chain A: D.295, E.297, Y.478, D.482 Ligands: CA.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parkash, V. et al., A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides. Nucleic Acids Res. (2023)

Release Date

2023-10-25

Peptides

DNA polymerase epsilon catalytic subunit A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase epsilon catalytic subunit A

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