Magnesium in PDB 8oi7: Trichomonas Vaginalis Riboside Hydrolase

The structure of Trichomonas Vaginalis Riboside Hydrolase, PDB code: 8oi7 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)	46.32 / 1.85
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.344, 92.344, 185.111, 90, 90, 90
R / Rfree (%)	18.4 / 20.1

The structure of Trichomonas Vaginalis Riboside Hydrolase also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Magnesium atom in the Trichomonas Vaginalis Riboside Hydrolase (pdb code 8oi7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Trichomonas Vaginalis Riboside Hydrolase, PDB code: 8oi7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Trichomonas Vaginalis Riboside Hydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trichomonas Vaginalis Riboside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:29.7 occ:1.00 O A:LEU28 2.2 33.0 1.0 O A:SER25 2.3 31.5 1.0 O A:VAL23 2.4 26.5 1.0 O A:HOH680 2.4 47.5 1.0 O A:ALA22 2.5 24.1 1.0 C A:VAL23 3.0 26.6 1.0 C A:LEU28 3.3 29.9 1.0 C A:SER25 3.4 31.0 1.0 CA A:VAL23 3.5 25.3 1.0 C A:ALA22 3.6 24.6 1.0 N A:SER25 3.8 29.5 1.0 N A:TYR24 4.0 27.0 1.0 N A:VAL23 4.0 24.8 1.0 C A:TYR24 4.1 29.7 1.0 CA A:SER25 4.1 29.7 1.0 CA A:LEU28 4.1 29.2 1.0 CB A:LEU28 4.2 28.1 1.0 N A:LEU28 4.2 29.2 1.0 O A:HOH654 4.3 53.2 1.0 N A:ASP29 4.4 29.4 1.0 O A:HOH670 4.4 60.6 1.0 CA A:TYR24 4.4 28.3 1.0 N A:PRO26 4.4 31.9 1.0 CB A:SER25 4.6 29.9 1.0 CA A:ASP29 4.6 29.8 1.0 O A:TYR24 4.6 32.2 1.0 CA A:PRO26 4.6 33.2 1.0 CG2 A:VAL30 4.7 25.7 1.0 N A:VAL30 4.7 25.4 1.0 CA A:ALA22 4.9 24.2 1.0 CB A:VAL23 4.9 25.6 1.0 C A:PRO26 4.9 33.1 1.0

Magnesium binding site 2 out of 2 in the Trichomonas Vaginalis Riboside Hydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trichomonas Vaginalis Riboside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:50.6 occ:1.00 O B:VAL23 2.1 51.6 1.0 O B:SER25 2.4 59.1 1.0 O B:ALA22 2.5 54.1 1.0 O B:LEU28 2.5 53.4 1.0 C B:VAL23 2.8 54.2 1.0 CA B:VAL23 3.3 52.5 1.0 C B:SER25 3.4 62.0 1.0 C B:ALA22 3.5 51.5 1.0 C B:LEU28 3.6 55.2 1.0 N B:SER25 3.7 58.2 1.0 N B:TYR24 3.7 54.7 1.0 N B:VAL23 3.8 51.4 1.0 C B:TYR24 3.9 59.4 1.0 CA B:SER25 4.1 59.6 1.0 CA B:TYR24 4.2 58.0 1.0 CA B:LEU28 4.4 55.8 1.0 CB B:LEU28 4.4 53.6 1.0 N B:PRO26 4.5 63.5 1.0 N B:LEU28 4.5 58.0 1.0 O B:TYR24 4.5 60.7 1.0 CB B:SER25 4.6 59.0 1.0 N B:ASP29 4.6 54.2 1.0 CB B:VAL23 4.7 53.6 1.0 CG2 B:VAL30 4.7 50.6 1.0 CA B:PRO26 4.7 64.8 1.0 CA B:ASP29 4.8 56.1 1.0 CA B:ALA22 4.8 49.8 1.0 N B:VAL30 4.9 51.4 1.0 CG1 B:VAL23 4.9 55.8 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