Calcium 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
Nickel	(Ni)	1 atom

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

Calcium 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 Calcium with other atoms in the Ca 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:Ca401 b:27.9 occ:1.00 O A:THR142 2.4 27.5 1.0 O2' A:38T402 2.4 32.8 1.0 OD2 A:ASP263 2.4 29.0 1.0 O A:HOH527 2.4 27.9 1.0 OD1 A:ASP10 2.4 30.9 1.0 OD1 A:ASP15 2.4 28.4 1.0 OD2 A:ASP15 2.4 27.9 1.0 O3' A:38T402 2.5 28.0 1.0 CG A:ASP15 2.7 27.6 1.0 O A:HOH595 3.3 47.6 1.0 CG A:ASP263 3.4 30.0 1.0 C2' A:38T402 3.4 34.1 1.0 C3' A:38T402 3.5 32.0 1.0 CG A:ASP10 3.5 35.4 1.0 C A:THR142 3.5 27.3 1.0 OD1 A:ASP263 3.7 28.6 1.0 OD2 A:ASP10 4.0 38.7 1.0 C1' A:38T402 4.1 38.7 1.0 OG1 A:THR142 4.2 30.5 1.0 CB A:ASP15 4.2 28.1 1.0 CA A:GLY143 4.3 26.3 1.0 N A:GLY143 4.3 28.5 1.0 CB A:THR142 4.4 29.3 1.0 O A:ASP10 4.5 32.0 1.0 ND2 A:ASN184 4.5 27.7 1.0 OD1 A:ASN184 4.5 28.8 1.0 C4' A:38T402 4.5 32.3 1.0 CA A:THR142 4.6 27.9 1.0 N A:ASP10 4.6 30.6 1.0 N A:ASP15 4.7 27.5 1.0 CB A:ASP263 4.7 27.6 1.0 O A:HOH511 4.8 41.0 1.0 C A:ASP10 4.8 29.6 1.0 CB A:ASP10 4.8 33.0 1.0 CA A:ASP15 4.9 28.6 1.0 O4' A:38T402 4.9 35.6 1.0 CB A:ASP14 4.9 38.4 1.0 CG A:ASN184 4.9 28.9 1.0 CA A:ASP10 5.0 30.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca401 b:41.7 occ:1.00 OD2 B:ASP263 2.4 41.3 1.0 O B:THR142 2.4 40.1 1.0 O2' B:38T402 2.4 44.8 1.0 O B:HOH507 2.4 33.5 1.0 OD2 B:ASP15 2.4 47.7 1.0 O3' B:38T402 2.4 42.5 1.0 OD1 B:ASP10 2.4 45.5 1.0 OD1 B:ASP15 2.4 46.5 1.0 CG B:ASP15 2.7 47.0 1.0 CG B:ASP263 3.4 42.6 1.0 C2' B:38T402 3.4 45.7 1.0 C3' B:38T402 3.5 43.4 1.0 CG B:ASP10 3.5 49.0 1.0 C B:THR142 3.6 40.3 1.0 OD1 B:ASP263 3.7 44.2 1.0 OD2 B:ASP10 3.9 46.7 1.0 C1' B:38T402 4.1 47.0 1.0 CB B:ASP15 4.2 47.9 1.0 OG1 B:THR142 4.2 44.3 1.0 CA B:GLY143 4.3 38.7 1.0 N B:GLY143 4.3 38.3 1.0 CB B:THR142 4.4 43.5 1.0 OD1 B:ASN184 4.5 43.0 1.0 ND2 B:ASN184 4.5 38.5 1.0 O B:ASP10 4.5 45.0 1.0 C4' B:38T402 4.5 43.1 1.0 CA B:THR142 4.6 40.8 1.0 N B:ASP10 4.6 47.7 1.0 N B:ASP15 4.7 48.7 1.0 CB B:ASP263 4.7 45.1 1.0 O B:HOH517 4.8 53.5 1.0 CB B:ASP10 4.8 47.4 1.0 C B:ASP10 4.8 47.7 1.0 CA B:ASP15 4.8 47.7 1.0 CB B:ASP14 4.9 59.0 1.0 CG B:ASN184 5.0 40.0 1.0 O4' B:38T402 5.0 43.8 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