SMTL ID : 8b7e.1 (1 other biounit)

The crystal structure of N828V variant of DNA Pol Epsilon containing UTP in the polymerase active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.1: 19 residues within 4Å: Chain A: Y.436, D.645, V.646, A.647, S.648, M.649, Y.650, P.651, R.786, K.790, K.829, V.833, Y.836, D.882 Chain B: C.11 Chain C: A.5, G.6 Ligands: CA.2, CA.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.645, A:S.648, A:S.648, A:M.649, A:Y.650 Water bridges: A:K.790 Salt bridges: A:R.786, A:R.786, A:K.790, A:K.829, A:K.829, A:K.829

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.645, V.646, D.882 Ligands: UTP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.645, A:V.646, A:D.882 CA.3: 3 residues within 4Å: Chain A: D.645, K.790 Ligands: UTP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.645, H2O.1, H2O.2

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain B: A.3 Chain C: G.12, G.13 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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