Nickel in PDB 8oi9: Trichomonas Vaginalis Riboside Hydrolase in Complex with 5- Methyluridine

The structure of Trichomonas Vaginalis Riboside Hydrolase in Complex with 5- Methyluridine, PDB code: 8oi9 was solved by M.Patrone, B.J.Stockman, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.29 / 1.95
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.49, 92.49, 186.884, 90, 90, 90
R / Rfree (%)	17.3 / 20.4

The structure of Trichomonas Vaginalis Riboside Hydrolase in Complex with 5- Methyluridine also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Nickel atom in the Trichomonas Vaginalis Riboside Hydrolase in Complex with 5- Methyluridine (pdb code 8oi9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Trichomonas Vaginalis Riboside Hydrolase in Complex with 5- Methyluridine, PDB code: 8oi9:

Nickel binding site 1 out of 1 in the Trichomonas Vaginalis Riboside Hydrolase in Complex with 5- Methyluridine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Trichomonas Vaginalis Riboside Hydrolase in Complex with 5- Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni405 b:60.7 occ:1.00 OE2 B:GLU85 1.9 76.8 1.0 O B:HOH556 1.9 65.2 1.0 ND1 B:HIS83 1.9 64.9 1.0 SG B:CYS79 2.3 63.4 1.0 CE1 B:HIS83 2.8 65.6 1.0 CG B:HIS83 3.1 64.5 1.0 CB B:CYS79 3.1 55.7 1.0 CD B:GLU85 3.1 71.3 1.0 CB B:HIS83 3.5 61.4 1.0 OE1 B:GLU85 3.8 72.6 1.0 NE2 B:HIS83 4.0 64.8 1.0 CD2 B:HIS83 4.1 64.9 1.0 CG B:GLU85 4.2 65.7 1.0 CA B:CYS79 4.3 50.1 1.0

M.Patrone, G.S.Galasyn, F.Kerin, M.M.Nyitray, D.W.Parkin, B.J.Stockman, M.Degano. A Riboside Hydrolase That Salvages Both Nucleobases and Nicotinamide in the Auxotrophic Parasite Trichomonas Vaginalis. J.Biol.Chem. 05077 2023.
ISSN: ESSN 1083-351X
PubMed: 37482279
DOI: 10.1016/J.JBC.2023.105077