Magnesium 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:

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

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Trichomonas Vaginalis Riboside Hydrolase in Complex with 5- Methyluridine, PDB code: 8oi9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Trichomonas Vaginalis Riboside Hydrolase in Complex with 5- Methyluridine


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 in Complex with 5- Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:34.7 occ:1.00 O A:LEU28 2.2 38.9 1.0 O A:SER25 2.3 37.6 1.0 O A:VAL23 2.4 30.2 1.0 O A:ALA22 2.5 29.7 1.0 O2 A:PIN403 2.6 50.3 1.0 C A:VAL23 3.1 31.1 1.0 O3 A:PIN403 3.4 70.2 1.0 C A:LEU28 3.4 35.4 1.0 S1 A:PIN403 3.4 61.2 1.0 C A:SER25 3.4 36.6 1.0 CA A:VAL23 3.5 31.0 1.0 C A:ALA22 3.6 29.9 1.0 N A:SER25 3.8 34.0 1.0 N A:TYR24 4.0 29.7 1.0 N A:VAL23 4.0 31.8 1.0 CA A:SER25 4.1 34.7 1.0 C A:TYR24 4.1 33.1 1.0 CA A:LEU28 4.2 32.8 1.0 O1 A:PIN403 4.2 59.2 1.0 CB A:LEU28 4.2 31.5 1.0 N A:LEU28 4.3 32.8 1.0 N A:ASP29 4.4 34.7 1.0 CA A:TYR24 4.4 31.6 1.0 N A:PRO26 4.5 37.1 1.0 CG2 A:VAL30 4.6 30.5 1.0 CB A:SER25 4.6 36.4 1.0 CA A:ASP29 4.6 33.6 1.0 N A:VAL30 4.7 30.8 1.0 CA A:PRO26 4.7 37.7 1.0 O A:TYR24 4.7 35.7 1.0 O A:HOH574 4.8 38.7 1.0 CA A:ALA22 4.9 28.0 1.0 CB A:VAL23 4.9 32.4 1.0 C1 A:PIN403 4.9 67.3 1.0 C A:PRO26 5.0 36.7 1.0

Magnesium binding site 2 out of 2 in the Trichomonas Vaginalis Riboside Hydrolase in Complex with 5- Methyluridine


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 in Complex with 5- Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:64.6 occ:1.00 O B:VAL23 2.3 59.7 1.0 O B:LEU28 2.3 62.5 1.0 O B:SER25 2.3 64.2 1.0 O B:ALA22 2.4 53.2 1.0 O1 B:SO4403 2.8 88.5 1.0 C B:VAL23 2.9 57.4 1.0 CA B:VAL23 3.4 54.9 1.0 C B:SER25 3.4 64.2 1.0 C B:ALA22 3.5 53.4 1.0 C B:LEU28 3.5 60.5 1.0 S B:SO4403 3.7 95.6 1.0 O2 B:SO4403 3.7 97.1 1.0 N B:SER25 3.7 62.6 1.0 N B:TYR24 3.8 57.5 1.0 O3 B:SO4403 3.9 94.9 1.0 N B:VAL23 3.9 53.7 1.0 C B:TYR24 4.1 62.7 1.0 CA B:SER25 4.1 63.9 1.0 CA B:LEU28 4.3 59.1 1.0 CB B:LEU28 4.3 56.2 1.0 CA B:TYR24 4.3 60.9 1.0 N B:LEU28 4.4 60.7 1.0 N B:PRO26 4.5 66.8 1.0 N B:ASP29 4.5 58.6 1.0 CG2 B:VAL30 4.5 52.7 1.0 CB B:SER25 4.6 63.2 1.0 O B:TYR24 4.7 64.0 1.0 CA B:ASP29 4.7 58.0 1.0 CA B:PRO26 4.7 67.9 1.0 N B:VAL30 4.7 51.9 1.0 CB B:VAL23 4.8 55.0 1.0 CA B:ALA22 4.8 52.7 1.0 O4 B:SO4403 5.0 92.3 1.0 C B:PRO26 5.0 67.5 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