Calcium in PDB 3t8i: Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase

All present enzymatic activity of Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase:
3.2.2.1;

The structure of Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase, PDB code: 3t8i was solved by C.Minici, G.Cacciapuoti, E.De Leo, M.Porcelli, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.23 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.760, 81.130, 98.020, 90.00, 100.70, 90.00
R / Rfree (%)	17 / 21.4

The binding sites of Calcium atom in the Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase (pdb code 3t8i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase, PDB code: 3t8i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:13.3 occ:1.00 O A:ILE121 2.3 17.1 1.0 O A:HOH391 2.5 26.4 1.0 OD2 A:ASP14 2.5 18.5 1.0 OD1 A:ASP9 2.5 15.3 1.0 OD2 A:ASP238 2.5 17.3 1.0 O A:HOH356 2.6 17.1 1.0 OD1 A:ASP14 2.6 15.6 1.0 O3 A:GOL307 2.7 17.9 1.0 CG A:ASP14 2.9 17.6 1.0 CG A:ASP238 3.5 17.9 1.0 C A:ILE121 3.5 14.9 1.0 CG A:ASP9 3.6 15.5 1.0 C3 A:GOL307 3.7 23.1 1.0 ND2 A:ASN36 3.8 17.0 1.0 OD1 A:ASP238 3.8 17.7 1.0 OD2 A:ASP9 4.0 13.9 1.0 CA A:SER122 4.3 14.8 1.0 N A:SER122 4.3 15.1 1.0 CB A:ASP14 4.4 16.2 1.0 O A:HOH351 4.5 21.3 1.0 O2 A:GOL307 4.5 34.3 1.0 CB A:ILE121 4.5 14.9 1.0 O A:ASP9 4.6 14.5 1.0 CA A:ILE121 4.6 14.1 1.0 CB A:SER122 4.6 15.0 1.0 N A:ASP9 4.6 14.3 1.0 C2 A:GOL307 4.7 25.4 1.0 CG1 A:ILE121 4.7 14.4 1.0 OD1 A:ASN163 4.7 15.2 1.0 CG A:ASN36 4.7 15.8 1.0 CB A:ASP238 4.8 15.7 1.0 ND2 A:ASN163 4.8 12.6 1.0 CB A:ASP9 4.9 14.8 1.0 CD1 A:ILE121 5.0 13.1 1.0

Calcium binding site 2 out of 4 in the Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:14.9 occ:1.00 O B:ILE121 2.2 15.9 1.0 OD2 B:ASP238 2.4 16.9 1.0 O B:HOH338 2.5 23.4 1.0 OD1 B:ASP9 2.5 17.2 1.0 OD2 B:ASP14 2.5 15.7 1.0 OD1 B:ASP14 2.7 17.6 1.0 O3 B:GOL307 2.7 18.0 1.0 O B:HOH322 2.7 16.9 1.0 CG B:ASP14 2.9 15.7 1.0 CG B:ASP238 3.4 17.5 1.0 C B:ILE121 3.5 15.8 1.0 CG B:ASP9 3.5 15.7 1.0 C3 B:GOL307 3.7 22.9 1.0 OD1 B:ASP238 3.7 17.2 1.0 ND2 B:ASN36 3.8 17.8 1.0 OD2 B:ASP9 3.9 17.3 1.0 CA B:SER122 4.2 14.6 1.0 N B:SER122 4.2 14.9 1.0 CB B:ASP14 4.4 15.7 1.0 O B:HOH361 4.4 18.6 1.0 CB B:ILE121 4.5 15.2 1.0 CB B:SER122 4.5 15.4 1.0 CA B:ILE121 4.5 14.9 1.0 N B:ASP9 4.5 16.1 1.0 O B:ASP9 4.7 17.3 1.0 O2 B:GOL307 4.7 32.3 1.0 CG1 B:ILE121 4.7 16.5 1.0 OD1 B:ASN163 4.7 16.5 1.0 C2 B:GOL307 4.7 26.0 1.0 CB B:ASP238 4.8 16.5 1.0 CG B:ASN36 4.8 16.9 1.0 ND2 B:ASN163 4.8 13.7 1.0 CB B:ASP9 4.9 16.5 1.0 CD1 B:ILE121 4.9 12.3 1.0

Calcium binding site 3 out of 4 in the Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca400 b:23.2 occ:1.00 O C:ILE121 2.2 23.4 1.0 OD2 C:ASP238 2.4 25.8 1.0 OD1 C:ASP9 2.4 26.3 1.0 O C:HOH360 2.4 30.4 1.0 OD2 C:ASP14 2.5 27.3 1.0 OD1 C:ASP14 2.5 22.1 1.0 O C:HOH334 2.7 23.4 1.0 O3 C:GOL307 2.7 33.0 1.0 CG C:ASP14 2.8 27.3 1.0 C C:ILE121 3.4 22.2 1.0 CG C:ASP238 3.5 26.6 1.0 CG C:ASP9 3.5 24.5 1.0 C3 C:GOL307 3.7 35.6 1.0 ND2 C:ASN36 3.7 26.7 1.0 OD1 C:ASP238 3.9 28.0 1.0 OD2 C:ASP9 3.9 21.3 1.0 N C:SER122 4.3 21.7 1.0 CA C:SER122 4.3 21.7 1.0 O C:HOH363 4.3 33.0 1.0 CB C:ASP14 4.3 27.2 1.0 O2 C:GOL307 4.4 39.0 1.0 CA C:ILE121 4.5 24.2 1.0 N C:ASP9 4.6 25.6 1.0 CB C:ILE121 4.6 24.5 1.0 CB C:SER122 4.6 21.7 1.0 C2 C:GOL307 4.7 36.7 1.0 CG C:ASN36 4.7 29.6 1.0 O C:ASP9 4.7 26.4 1.0 OD1 C:ASN163 4.7 23.7 1.0 CB C:ASP238 4.8 27.1 1.0 CB C:ASP9 4.8 25.4 1.0 CG1 C:ILE121 4.9 24.5 1.0 CD1 C:ILE121 5.0 24.9 1.0 CA C:ASP14 5.0 27.5 1.0 ND2 C:ASN163 5.0 23.1 1.0 OD1 C:ASN36 5.0 31.2 1.0

Calcium binding site 4 out of 4 in the Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Analysis of Thermostable S. Solfataricus Purine-Specific Nucleoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca400 b:19.7 occ:1.00 O D:ILE121 2.2 24.2 1.0 O D:HOH332 2.4 34.2 1.0 OD2 D:ASP238 2.4 26.9 1.0 OD2 D:ASP14 2.5 22.8 1.0 OD1 D:ASP9 2.6 22.7 1.0 O D:HOH347 2.6 24.3 1.0 O3 D:GOL307 2.6 27.2 1.0 OD1 D:ASP14 2.7 22.5 1.0 CG D:ASP14 2.9 21.3 1.0 CG D:ASP238 3.4 24.6 1.0 C D:ILE121 3.4 22.5 1.0 CG D:ASP9 3.7 22.8 1.0 OD1 D:ASP238 3.7 21.4 1.0 C3 D:GOL307 3.8 30.7 1.0 ND2 D:ASN36 3.8 23.4 1.0 OD2 D:ASP9 4.1 20.5 1.0 CA D:SER122 4.2 21.6 1.0 N D:SER122 4.2 22.7 1.0 CB D:ASP14 4.4 24.1 1.0 O2 D:GOL307 4.4 38.0 1.0 O D:HOH345 4.4 20.8 1.0 CB D:SER122 4.4 22.0 1.0 CB D:ILE121 4.5 23.1 1.0 CA D:ILE121 4.5 22.6 1.0 N D:ASP9 4.6 22.2 1.0 CG1 D:ILE121 4.6 23.3 1.0 O D:ASP9 4.6 24.2 1.0 C2 D:GOL307 4.6 31.5 1.0 OD1 D:ASN163 4.7 20.0 1.0 CB D:ASP238 4.8 23.0 1.0 CG D:ASN36 4.8 25.9 1.0 ND2 D:ASN163 4.8 20.7 1.0 CD1 D:ILE121 4.9 22.5 1.0 CB D:ASP9 5.0 22.9 1.0

C.Minici, G.Cacciapuoti, E.De Leo, M.Porcelli, M.Degano. New Determinants in the Catalytic Mechanism of Nucleoside Hydrolases From the Structures of Two Isozymes From Sulfolobus Solfataricus. Biochemistry V. 51 4590 2012.
ISSN: ISSN 0006-2960
PubMed: 22551416
DOI: 10.1021/BI300209G