Calcium in PDB 8oia: Trichomonas Vaginalis Riboside Hydrolase in Complex with D-Ribose

The structure of Trichomonas Vaginalis Riboside Hydrolase in Complex with D-Ribose, PDB code: 8oia 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)	43.98 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.995, 135.622, 94.075, 90, 104.69, 90
R / Rfree (%)	23.4 / 27

The binding sites of Calcium atom in the Trichomonas Vaginalis Riboside Hydrolase in Complex with D-Ribose (pdb code 8oia). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Trichomonas Vaginalis Riboside Hydrolase in Complex with D-Ribose, PDB code: 8oia:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Trichomonas Vaginalis Riboside Hydrolase in Complex with D-Ribose


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 D-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:23.9 occ:1.00 O A:THR142 2.4 21.1 1.0 OD1 A:ASP10 2.4 24.6 1.0 O2 A:RIB402 2.4 20.9 1.0 OD2 A:ASP263 2.5 18.3 1.0 OD1 A:ASP15 2.5 26.4 1.0 O3 A:RIB402 2.5 23.3 1.0 OD2 A:ASP15 2.5 23.1 1.0 O A:HOH505 2.7 18.6 1.0 CG A:ASP15 2.8 27.7 1.0 CG A:ASP263 3.4 19.6 1.0 C2 A:RIB402 3.5 25.5 1.0 CG A:ASP10 3.5 23.7 1.0 C3 A:RIB402 3.5 27.3 1.0 C A:THR142 3.5 26.5 1.0 OD1 A:ASP263 3.7 21.4 1.0 OD2 A:ASP10 3.8 22.1 1.0 CA A:GLY143 4.1 25.0 1.0 OG1 A:THR142 4.2 24.9 1.0 N A:GLY143 4.2 25.4 1.0 CB A:ASP15 4.3 29.6 1.0 CB A:THR142 4.4 25.8 1.0 C4 A:RIB402 4.4 32.5 1.0 OD1 A:ASN184 4.5 30.5 1.0 N A:ASP10 4.5 24.0 1.0 ND2 A:ASN184 4.5 24.8 1.0 O A:ASP10 4.5 30.6 1.0 C1 A:RIB402 4.6 28.2 1.0 CA A:THR142 4.6 28.1 1.0 O4 A:RIB402 4.7 28.9 1.0 N A:ASP15 4.7 28.7 1.0 CB A:ASP10 4.8 24.5 1.0 CB A:ASP263 4.8 21.5 1.0 C A:ASP10 4.8 29.2 1.0 CA A:ASP15 4.9 28.9 1.0 CA A:ASP10 4.9 26.0 1.0 CB A:ASP14 4.9 29.4 1.0 CG A:ASN184 5.0 27.8 1.0 O1 A:RIB402 5.0 30.5 1.0

Calcium binding site 2 out of 4 in the Trichomonas Vaginalis Riboside Hydrolase in Complex with D-Ribose


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 D-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:21.6 occ:1.00 O B:HOH519 2.3 22.4 1.0 O3 B:RIB402 2.3 22.0 1.0 O B:THR142 2.4 20.1 1.0 OD1 B:ASP15 2.4 21.9 1.0 OD1 B:ASP10 2.4 21.3 1.0 OD2 B:ASP263 2.4 21.5 1.0 OD2 B:ASP15 2.5 19.5 1.0 O2 B:RIB402 2.6 17.9 1.0 CG B:ASP15 2.8 22.4 1.0 CG B:ASP263 3.4 22.9 1.0 ND2 B:ASN39 3.4 20.8 1.0 CG B:ASP10 3.5 22.3 1.0 C3 B:RIB402 3.5 22.9 1.0 C B:THR142 3.5 20.1 1.0 C2 B:RIB402 3.6 21.7 1.0 OD1 B:ASP263 3.8 21.3 1.0 OD2 B:ASP10 3.9 23.6 1.0 OG1 B:THR142 4.2 21.5 1.0 CA B:GLY143 4.2 22.4 1.0 N B:GLY143 4.2 23.4 1.0 OD1 B:ASP14 4.2 23.5 1.0 CB B:ASP15 4.2 22.9 1.0 CB B:THR142 4.4 19.5 1.0 O B:ASP10 4.4 26.6 1.0 C4 B:RIB402 4.5 27.3 1.0 CG B:ASN39 4.5 22.7 1.0 OD1 B:ASN184 4.5 16.2 1.0 ND2 B:ASN184 4.5 16.0 1.0 OD2 B:ASP14 4.5 21.3 1.0 N B:ASP10 4.5 20.5 1.0 O4 B:RIB402 4.6 22.1 1.0 CA B:THR142 4.6 19.2 1.0 CG B:ASP14 4.6 21.6 1.0 C1 B:RIB402 4.7 20.9 1.0 N B:ASP15 4.7 25.9 1.0 C B:ASP10 4.7 23.3 1.0 CB B:ASP10 4.8 22.6 1.0 CB B:ASP263 4.8 26.0 1.0 OD1 B:ASN39 4.9 21.7 1.0 CA B:ASP15 4.9 24.6 1.0 CA B:ASP10 4.9 21.7 1.0 CG B:ASN184 5.0 18.1 1.0 O1 B:RIB402 5.0 23.4 1.0

Calcium binding site 3 out of 4 in the Trichomonas Vaginalis Riboside Hydrolase in Complex with D-Ribose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Trichomonas Vaginalis Riboside Hydrolase in Complex with D-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:22.1 occ:1.00 OD1 C:ASP10 2.4 24.2 1.0 O C:THR142 2.4 23.4 1.0 O3 C:RIB402 2.4 24.7 1.0 OD1 C:ASP15 2.4 26.0 1.0 OD2 C:ASP263 2.4 27.9 1.0 O C:HOH518 2.4 25.6 1.0 OD2 C:ASP15 2.5 26.2 1.0 O2 C:RIB402 2.5 20.5 1.0 CG C:ASP15 2.7 30.9 1.0 CG C:ASP263 3.4 25.8 1.0 CG C:ASP10 3.4 21.9 1.0 ND2 C:ASN39 3.5 19.2 1.0 C C:THR142 3.5 24.5 1.0 C3 C:RIB402 3.5 22.5 1.0 C2 C:RIB402 3.5 21.2 1.0 OD1 C:ASP263 3.8 24.7 1.0 OD2 C:ASP10 3.9 23.5 1.0 OG1 C:THR142 4.1 19.4 1.0 CA C:GLY143 4.1 29.8 1.0 N C:GLY143 4.2 30.3 1.0 CB C:ASP15 4.2 27.0 1.0 OD1 C:ASP14 4.2 20.6 1.0 CB C:THR142 4.4 21.3 1.0 O C:ASP10 4.4 21.2 1.0 N C:ASP10 4.5 17.9 1.0 ND2 C:ASN184 4.5 16.0 1.0 CG C:ASN39 4.5 20.0 1.0 OD2 C:ASP14 4.5 24.2 1.0 OD1 C:ASN184 4.5 15.6 1.0 C4 C:RIB402 4.5 22.7 1.0 CA C:THR142 4.6 21.3 1.0 C1 C:RIB402 4.7 19.3 1.0 CG C:ASP14 4.7 21.4 1.0 N C:ASP15 4.7 24.1 1.0 CB C:ASP10 4.7 20.7 1.0 C C:ASP10 4.7 21.2 1.0 O4 C:RIB402 4.7 20.1 1.0 CB C:ASP263 4.8 28.9 1.0 OD1 C:ASN39 4.9 20.4 1.0 CA C:ASP10 4.9 20.4 1.0 CA C:ASP15 4.9 23.6 1.0 O1 C:RIB402 4.9 21.6 1.0 CG C:ASN184 5.0 18.7 1.0

Calcium binding site 4 out of 4 in the Trichomonas Vaginalis Riboside Hydrolase in Complex with D-Ribose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Trichomonas Vaginalis Riboside Hydrolase in Complex with D-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:23.1 occ:1.00 O D:THR142 2.4 19.6 1.0 OD2 D:ASP263 2.4 21.8 1.0 O2 D:RIB402 2.4 23.2 1.0 O3 D:RIB402 2.4 23.1 1.0 OD1 D:ASP10 2.4 21.2 1.0 OD1 D:ASP15 2.4 24.8 1.0 OD2 D:ASP15 2.5 26.8 1.0 O D:HOH509 2.6 18.2 1.0 CG D:ASP15 2.7 28.6 1.0 CG D:ASP263 3.4 22.5 1.0 C2 D:RIB402 3.4 26.9 1.0 C3 D:RIB402 3.5 26.1 1.0 CG D:ASP10 3.5 23.3 1.0 C D:THR142 3.5 25.1 1.0 OD1 D:ASP263 3.7 23.1 1.0 OD2 D:ASP10 3.8 20.6 1.0 OG1 D:THR142 4.1 22.1 1.0 CA D:GLY143 4.2 26.5 1.0 N D:GLY143 4.2 25.5 1.0 CB D:ASP15 4.2 31.0 1.0 CB D:THR142 4.4 25.0 1.0 C4 D:RIB402 4.4 28.6 1.0 OD1 D:ASN184 4.5 24.7 1.0 ND2 D:ASN184 4.5 23.1 1.0 N D:ASP10 4.5 29.3 1.0 C1 D:RIB402 4.6 27.2 1.0 O D:ASP10 4.6 30.6 1.0 CA D:THR142 4.6 24.6 1.0 O4 D:RIB402 4.6 28.1 1.0 N D:ASP15 4.7 30.2 1.0 CB D:ASP263 4.7 21.5 1.0 CB D:ASP10 4.8 24.6 1.0 C D:ASP10 4.8 30.8 1.0 CA D:ASP15 4.9 30.8 1.0 CB D:ASP14 4.9 37.5 1.0 O1 D:RIB402 4.9 27.7 1.0 CA D:ASP10 5.0 27.4 1.0 CG D:ASN184 5.0 25.0 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