Calcium in PDB 8rih: Crystal Structure of the Saccharomyces Cerevisiae URH1P Riboside Hydrolase

The structure of Crystal Structure of the Saccharomyces Cerevisiae URH1P Riboside Hydrolase, PDB code: 8rih was solved by M.Degano, A.A.Carriles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	121.49 / 2.74
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	140.284, 140.284, 81.343, 90, 90, 120
R / Rfree (%)	18.6 / 22.5

The binding sites of Calcium atom in the Crystal Structure of the Saccharomyces Cerevisiae URH1P Riboside Hydrolase (pdb code 8rih). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Saccharomyces Cerevisiae URH1P Riboside Hydrolase, PDB code: 8rih:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Saccharomyces Cerevisiae URH1P Riboside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Saccharomyces Cerevisiae URH1P Riboside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:24.9 occ:1.00 OD2 A:ASP18 2.4 23.1 1.0 O A:THR130 2.4 24.5 1.0 OD1 A:ASP13 2.4 24.5 1.0 O A:HOH502 2.4 8.6 1.0 OD2 A:ASP255 2.4 24.2 1.0 OD1 A:ASP18 2.4 25.0 1.0 O2 A:TRS401 2.4 12.1 1.0 CG A:ASP18 2.7 24.0 1.0 O A:HOH503 2.8 3.9 1.0 C A:THR130 3.2 23.1 1.0 CG A:ASP255 3.4 24.1 1.0 CG A:ASP13 3.5 26.1 1.0 OD1 A:ASP255 3.8 25.2 1.0 OG1 A:THR130 3.8 21.5 1.0 C2 A:TRS401 3.8 12.7 1.0 ND2 A:ASN42 3.8 31.2 1.0 N A:GLY131 3.9 23.0 1.0 OD2 A:ASP13 4.0 28.5 1.0 CA A:GLY131 4.0 24.1 1.0 CB A:THR130 4.1 21.3 1.0 CA A:THR130 4.2 21.7 1.0 CB A:ASP18 4.2 23.3 1.0 OD1 A:ASN175 4.3 23.7 1.0 ND2 A:ASN175 4.3 22.8 1.0 N A:ASP13 4.5 23.0 1.0 OD1 A:ASP17 4.5 26.1 1.0 O A:ASP13 4.6 25.7 1.0 CG A:ASN42 4.7 32.0 1.0 CB A:ASP255 4.8 23.1 1.0 CG A:ASN175 4.8 23.3 1.0 C A:TRS401 4.8 13.8 1.0 CB A:ASP13 4.8 25.8 1.0 OD2 A:ASP17 4.8 25.8 1.0 C3 A:TRS401 4.8 15.7 1.0 OD1 A:ASN42 4.9 32.1 1.0 C A:ASP13 4.9 25.3 1.0 N A:TRS401 4.9 13.0 1.0 O3 A:TRS401 5.0 20.3 1.0 CG A:ASP17 5.0 25.9 1.0 CA A:ASP18 5.0 22.6 1.0 CA A:ASP13 5.0 24.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Saccharomyces Cerevisiae URH1P Riboside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Saccharomyces Cerevisiae URH1P Riboside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:32.2 occ:1.00 OD1 B:ASP18 2.4 32.3 1.0 O B:THR130 2.4 31.4 1.0 OD2 B:ASP18 2.4 29.6 1.0 OD2 B:ASP255 2.4 30.7 1.0 O B:HOH502 2.4 7.2 1.0 O1 B:TRS401 2.4 19.6 1.0 OD1 B:ASP13 2.4 32.7 1.0 O B:HOH506 2.6 21.4 1.0 CG B:ASP18 2.7 30.5 1.0 C B:THR130 3.3 30.0 1.0 CG B:ASP255 3.4 30.4 1.0 CG B:ASP13 3.6 33.5 1.0 OD1 B:ASP255 3.8 31.5 1.0 C1 B:TRS401 3.8 24.4 1.0 ND2 B:ASN42 3.8 38.9 1.0 OG1 B:THR130 3.9 28.0 1.0 N B:GLY131 3.9 29.0 1.0 OD2 B:ASP13 4.0 34.4 1.0 CA B:GLY131 4.1 29.9 1.0 CB B:THR130 4.1 28.6 1.0 CA B:THR130 4.2 29.0 1.0 CB B:ASP18 4.2 29.4 1.0 OD1 B:ASN175 4.3 33.6 1.0 ND2 B:ASN175 4.4 32.0 1.0 OD1 B:ASP17 4.5 38.8 1.0 N B:ASP13 4.5 30.9 1.0 O B:ASP13 4.6 34.7 1.0 O2 B:TRS401 4.6 33.4 1.0 CG B:ASN42 4.7 41.0 1.0 CG B:ASN175 4.8 33.0 1.0 CB B:ASP255 4.8 29.2 1.0 OD2 B:ASP17 4.8 38.5 1.0 OD1 B:ASN42 4.8 43.3 1.0 CB B:ASP13 4.8 33.3 1.0 C B:TRS401 4.8 30.2 1.0 CG B:ASP17 4.9 38.6 1.0 C B:ASP13 4.9 33.0 1.0 N B:TRS401 4.9 26.1 1.0 CA B:ASP18 5.0 29.2 1.0

A.A.Carriles, L.Muzzolini, C.Minici, P.Tornaghi, M.Patrone, M.Degano. Structure-Function Insights Into the Dual Role in Nucleobase and Nicotinamide Metabolism and A Possible Use in Cancer Gene Therapy of the URH1P Riboside Hydrolase Int J Mol Sci 2024.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS25137032