Calcium 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
Magnesium	(Mg)	2 atoms

The binding sites of Calcium atom in the Trichomonas Vaginalis Riboside Hydrolase (pdb code 8oi7). 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, PDB code: 8oi7:
Jump to Calcium binding site number: 1; 2;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:26.4 occ:1.00 O A:THR142 2.4 25.4 1.0 OD2 A:ASP263 2.4 27.1 1.0 OD2 A:ASP10 2.4 27.2 1.0 O A:HOH628 2.4 29.7 1.0 O A:HOH575 2.4 27.8 1.0 O A:HOH536 2.4 23.7 1.0 OD1 A:ASP15 2.5 25.8 1.0 OD2 A:ASP15 2.5 24.6 1.0 CG A:ASP15 2.8 25.2 1.0 CG A:ASP263 3.4 26.5 1.0 CG A:ASP10 3.5 28.9 1.0 C A:THR142 3.6 25.0 1.0 O A:HOH603 3.6 45.6 1.0 OD1 A:ASP263 3.7 29.0 1.0 OD1 A:ASP10 4.0 30.5 1.0 OG1 A:THR142 4.2 26.2 1.0 CB A:ASP15 4.3 25.3 1.0 CA A:GLY143 4.3 25.4 1.0 N A:GLY143 4.3 25.1 1.0 CB A:THR142 4.4 25.2 1.0 O A:ASP10 4.5 27.1 1.0 O A:HOH711 4.5 58.6 1.0 ND2 A:ASN184 4.5 25.1 1.0 OD1 A:ASN184 4.5 24.6 1.0 CA A:THR142 4.6 25.4 1.0 N A:ASP10 4.6 26.0 1.0 O A:HOH527 4.6 37.8 1.0 N A:ASP15 4.7 26.1 1.0 CB A:ASP263 4.7 26.0 1.0 C A:ASP10 4.7 26.8 1.0 O A:HOH721 4.8 52.0 1.0 CB A:ASP10 4.8 27.8 1.0 CA A:ASP15 4.9 25.2 1.0 CA A:ASP10 5.0 26.7 1.0 CG A:ASN184 5.0 24.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:41.7 occ:1.00 OD2 B:ASP263 2.4 42.5 1.0 O B:HOH598 2.4 46.7 1.0 O B:THR142 2.4 39.4 1.0 O B:HOH510 2.4 38.2 1.0 O B:HOH543 2.4 31.1 1.0 OD2 B:ASP10 2.4 41.5 1.0 OD1 B:ASP15 2.4 45.3 1.0 OD2 B:ASP15 2.4 44.7 1.0 CG B:ASP15 2.7 44.2 1.0 CG B:ASP263 3.4 43.2 1.0 CG B:ASP10 3.5 42.8 1.0 C B:THR142 3.6 38.6 1.0 OD1 B:ASP263 3.7 44.5 1.0 OD1 B:ASP10 3.9 41.3 1.0 CB B:ASP15 4.2 45.1 1.0 OG1 B:THR142 4.2 38.9 1.0 CA B:GLY143 4.3 36.1 1.0 N B:GLY143 4.4 36.9 1.0 CB B:THR142 4.4 40.6 1.0 O B:ASP10 4.5 44.4 1.0 OD1 B:ASN184 4.5 37.5 1.0 ND2 B:ASN184 4.5 38.1 1.0 N B:ASP10 4.6 43.9 1.0 CA B:THR142 4.6 39.6 1.0 N B:ASP15 4.7 44.9 1.0 CB B:ASP263 4.7 44.3 1.0 C B:ASP10 4.8 44.9 1.0 CB B:ASP10 4.8 42.2 1.0 O B:HOH575 4.8 44.9 1.0 CA B:ASP15 4.9 45.5 1.0 CA B:ASP10 5.0 44.2 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