Calcium in PDB 8oib: Trichomonas Vaginalis Riboside Hydrolase in Complex with Glycerol

The structure of Trichomonas Vaginalis Riboside Hydrolase in Complex with Glycerol, PDB code: 8oib 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)	88.73 / 2.44
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.034, 156.998, 88.729, 90, 90.56, 90
R / Rfree (%)	18.9 / 22.6

The binding sites of Calcium atom in the Trichomonas Vaginalis Riboside Hydrolase in Complex with Glycerol (pdb code 8oib). 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 Glycerol, PDB code: 8oib:
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 Glycerol


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 Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:46.5 occ:1.00 O A:THR142 2.4 38.8 1.0 O3 A:GOL401 2.4 53.1 1.0 O A:HOH503 2.4 45.4 1.0 OD1 A:ASP10 2.4 43.3 1.0 OD2 A:ASP15 2.4 51.0 1.0 OD2 A:ASP263 2.4 46.4 1.0 OD1 A:ASP15 2.5 55.9 1.0 O A:HOH509 2.5 36.9 1.0 CG A:ASP15 2.8 53.5 1.0 CG A:ASP263 3.4 43.2 1.0 CG A:ASP10 3.5 44.7 1.0 C A:THR142 3.6 40.7 1.0 OD1 A:ASP263 3.7 42.7 1.0 C3 A:GOL401 3.8 60.4 1.0 OD2 A:ASP10 3.8 46.7 1.0 ND2 A:ASN39 4.0 83.3 1.0 OG1 A:THR142 4.3 42.0 1.0 CB A:ASP15 4.3 50.9 1.0 O2 A:GOL401 4.3 63.2 1.0 CA A:GLY143 4.4 45.9 1.0 N A:GLY143 4.4 43.9 1.0 OD1 A:ASN184 4.4 43.0 1.0 CB A:THR142 4.4 39.7 1.0 C2 A:GOL401 4.5 64.5 1.0 ND2 A:ASN184 4.5 44.9 1.0 CA A:THR142 4.6 40.5 1.0 O A:ASP10 4.6 40.3 1.0 N A:ASP10 4.6 49.7 1.0 CB A:ASP10 4.8 45.7 1.0 CB A:ASP263 4.8 44.5 1.0 CG A:ASN39 4.8 83.2 1.0 N A:ASP15 4.9 45.1 1.0 C A:ASP10 4.9 42.6 1.0 CG A:ASN184 4.9 43.5 1.0 OD1 A:ASN39 4.9 83.1 1.0 CA A:ASP15 5.0 47.9 1.0

Calcium binding site 2 out of 4 in the Trichomonas Vaginalis Riboside Hydrolase in Complex with Glycerol


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 Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:42.9 occ:1.00 O3 B:GOL401 2.4 60.5 1.0 O B:HOH511 2.4 41.5 1.0 OD2 B:ASP263 2.4 45.8 1.0 O B:THR142 2.4 37.2 1.0 OD1 B:ASP15 2.4 60.8 1.0 O B:HOH507 2.4 44.6 1.0 OD1 B:ASP10 2.5 44.5 1.0 OD2 B:ASP15 2.5 49.8 1.0 CG B:ASP15 2.8 55.6 1.0 CG B:ASP263 3.4 41.3 1.0 C3 B:GOL401 3.5 66.0 1.0 CG B:ASP10 3.5 48.3 1.0 C B:THR142 3.6 37.5 1.0 OD1 B:ASP263 3.7 46.1 1.0 OD2 B:ASP10 3.9 50.3 1.0 ND2 B:ASN39 4.0 80.5 1.0 CB B:ASP15 4.3 51.1 1.0 OG1 B:THR142 4.3 47.9 1.0 N B:GLY143 4.4 35.9 1.0 OD1 B:ASN184 4.4 39.8 1.0 CA B:GLY143 4.4 37.3 1.0 CB B:THR142 4.5 50.8 1.0 C2 B:GOL401 4.5 70.0 1.0 ND2 B:ASN184 4.6 42.6 1.0 CA B:THR142 4.6 43.7 1.0 O B:ASP10 4.6 43.4 1.0 N B:ASP10 4.7 49.3 1.0 O2 B:GOL401 4.7 85.0 1.0 CB B:ASP263 4.8 41.0 1.0 CB B:ASP10 4.8 47.3 1.0 N B:ASP15 4.9 42.7 1.0 CG B:ASN39 4.9 85.3 1.0 C B:ASP10 4.9 44.5 1.0 CG B:ASN184 5.0 45.4 1.0 CA B:ASP15 5.0 46.4 1.0 OD2 B:ASP14 5.0 108.6 1.0 OD1 B:ASN39 5.0 90.2 1.0 CB B:ASP14 5.0 60.0 1.0

Calcium binding site 3 out of 4 in the Trichomonas Vaginalis Riboside Hydrolase in Complex with Glycerol


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 Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca400 b:50.4 occ:1.00 O3 C:GOL401 2.4 56.6 1.0 O C:HOH518 2.4 39.9 1.0 OD2 C:ASP263 2.4 48.6 1.0 O C:THR142 2.4 42.1 1.0 OD2 C:ASP15 2.4 51.4 1.0 OD1 C:ASP15 2.4 53.0 1.0 OD1 C:ASP10 2.4 57.3 1.0 O C:HOH509 2.5 40.5 1.0 CG C:ASP15 2.8 50.5 1.0 CG C:ASP263 3.4 51.6 1.0 C3 C:GOL401 3.5 57.1 1.0 CG C:ASP10 3.5 55.2 1.0 C C:THR142 3.6 43.4 1.0 OD1 C:ASP263 3.7 50.4 1.0 OD2 C:ASP10 3.9 60.8 1.0 ND2 C:ASN39 4.0 72.3 1.0 CB C:ASP15 4.3 53.5 1.0 O2 C:GOL401 4.3 68.9 1.0 OG1 C:THR142 4.3 47.7 1.0 CA C:GLY143 4.4 48.7 1.0 N C:GLY143 4.4 46.6 1.0 OD1 C:ASN184 4.4 42.8 1.0 CB C:THR142 4.4 50.2 1.0 C2 C:GOL401 4.5 58.8 1.0 ND2 C:ASN184 4.6 42.3 1.0 O C:ASP10 4.6 48.8 1.0 CA C:THR142 4.6 46.8 1.0 N C:ASP10 4.6 49.4 1.0 CB C:ASP263 4.7 50.5 1.0 CB C:ASP10 4.8 53.6 1.0 N C:ASP15 4.8 51.7 1.0 CG C:ASN39 4.9 78.5 1.0 C C:ASP10 4.9 48.6 1.0 CA C:ASP15 4.9 55.6 1.0 CG C:ASN184 5.0 42.3 1.0 CB C:ASP14 5.0 65.8 1.0 OD1 C:ASN39 5.0 76.1 1.0

Calcium binding site 4 out of 4 in the Trichomonas Vaginalis Riboside Hydrolase in Complex with Glycerol


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 Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca400 b:65.5 occ:1.00 OD1 D:ASP10 2.4 66.2 1.0 O D:HOH507 2.4 58.4 1.0 O3 D:GOL401 2.4 80.9 1.0 OD2 D:ASP263 2.4 56.2 1.0 O D:THR142 2.5 51.9 1.0 O D:HOH510 2.5 43.6 1.0 OD2 D:ASP15 2.5 68.5 1.0 OD1 D:ASP15 2.5 69.7 1.0 CG D:ASP15 2.8 71.7 1.0 CG D:ASP263 3.4 51.5 1.0 CG D:ASP10 3.4 58.0 1.0 C D:THR142 3.6 46.6 1.0 OD1 D:ASP263 3.7 57.2 1.0 OD2 D:ASP10 3.8 67.5 1.0 C3 D:GOL401 3.8 73.6 1.0 ND2 D:ASN39 4.0 73.9 1.0 O2 D:GOL401 4.2 86.9 1.0 OG1 D:THR142 4.3 56.2 1.0 CB D:ASP15 4.3 65.9 1.0 CA D:GLY143 4.4 44.3 1.0 N D:GLY143 4.4 44.5 1.0 CB D:THR142 4.5 52.5 1.0 OD1 D:ASN184 4.5 47.8 1.0 C2 D:GOL401 4.6 72.5 1.0 O D:ASP10 4.6 46.6 1.0 N D:ASP10 4.6 49.5 1.0 CA D:THR142 4.6 47.2 1.0 ND2 D:ASN184 4.7 42.9 1.0 CB D:ASP10 4.8 53.5 1.0 CB D:ASP263 4.8 47.9 1.0 CG D:ASN39 4.8 74.1 1.0 C D:ASP10 4.9 50.6 1.0 N D:ASP15 4.9 56.5 1.0 OD1 D:ASN39 4.9 75.7 1.0 CA D:ASP15 5.0 62.5 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