Potassium in PDB 7oy3: Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp

The structure of Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp, PDB code: 7oy3 was solved by H.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.78 / 1.78
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.806, 106.806, 108.457, 90, 90, 120
R / Rfree (%)	17 / 19.4

The structure of Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Potassium atom in the Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp (pdb code 7oy3). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total only one binding site of Potassium was determined in the Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp, PDB code: 7oy3:

Potassium binding site 1 out of 1 in the Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:K601 b:26.6 occ:0.89 NE2 A:HIS241 2.0 25.9 1.0 ND1 A:HIS155 2.2 26.3 1.0 OA3 B:RGP71 2.3 34.7 0.7 OE1 A:GLU8 2.3 41.1 1.0 OE2 A:GLU8 2.4 40.4 1.0 CD A:GLU8 2.7 37.4 1.0 O3B A:ADP612 2.7 37.4 0.6 CE1 A:HIS241 2.8 22.3 1.0 CE1 A:HIS155 3.1 26.8 1.0 CD2 A:HIS241 3.1 22.3 1.0 CG A:HIS155 3.2 21.1 1.0 O B:HOH101 3.4 33.1 0.6 PA B:RGP71 3.5 32.7 0.3 CB A:HIS155 3.6 19.4 1.0 OA2 B:RGP71 3.7 35.3 0.6 PB A:ADP612 3.7 40.6 0.6 O2B A:ADP612 3.8 33.6 0.6 O A:HOH788 3.9 39.2 1.0 MG A:MG602 3.9 30.3 0.5 ND1 A:HIS241 4.0 27.1 1.0 O B:HOH128 4.0 44.6 1.0 CG A:HIS241 4.2 19.4 1.0 CG A:GLU8 4.2 29.1 1.0 O3A A:ADP612 4.2 38.2 0.6 NE2 A:HIS155 4.3 21.6 1.0 CD2 A:HIS155 4.3 21.9 1.0 NH2 A:ARG239 4.4 41.2 1.0 OA1 B:RGP71 4.5 35.9 0.6 OE2 B:RGP71 4.7 34.5 1.0 CB A:GLU8 4.8 22.4 1.0 OE1 B:RGP71 4.9 29.1 1.0 OD1 A:ASN157 5.0 21.8 1.0

H.Cui, A.U.Muller, M.Leibundgut, J.Tian, N.Ban, E.Weber-Ban. Structures of Prokaryotic Ubiquitin-Like Protein Pup in Complex with Depupylase Dop Reveal the Mechanism of Catalytic Phosphate Formation. Nat Commun V. 12 6635 2021.
ISSN: ESSN 2041-1723
PubMed: 34789727
DOI: 10.1038/S41467-021-26848-X