Sodium in PDB 8d38: Structure of A Purine Nucleoside Phosphorylase From Geobacillus Stearothermophilus

All present enzymatic activity of Structure of A Purine Nucleoside Phosphorylase From Geobacillus Stearothermophilus:
2.4.2.1;

The structure of Structure of A Purine Nucleoside Phosphorylase From Geobacillus Stearothermophilus, PDB code: 8d38 was solved by F.Given, J.Johnston, D.Crittenden, F.Moran, A.Johns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.05 / 1.72
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.963, 102.963, 167.763, 90, 90, 90
R / Rfree (%)	19.6 / 22.4

The binding sites of Sodium atom in the Structure of A Purine Nucleoside Phosphorylase From Geobacillus Stearothermophilus (pdb code 8d38). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of A Purine Nucleoside Phosphorylase From Geobacillus Stearothermophilus, PDB code: 8d38:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of A Purine Nucleoside Phosphorylase From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Purine Nucleoside Phosphorylase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:35.3 occ:1.00 O A:HOH505 2.2 45.1 1.0 OG A:SER2 2.2 34.0 1.0 O A:SER2 2.4 32.1 1.0 O A:ILE5 2.4 36.9 1.0 OH A:TYR80 2.7 33.4 1.0 CB A:SER2 3.2 30.8 1.0 C A:SER2 3.3 30.1 1.0 O A:MET1 3.6 33.5 1.0 C A:ILE5 3.6 36.0 1.0 CZ A:TYR80 3.7 36.7 1.0 CA A:SER2 3.7 30.5 1.0 CE2 A:TYR80 4.0 32.4 1.0 O A:HOH436 4.0 41.5 1.0 C A:MET1 4.3 36.0 1.0 O A:ALA7 4.3 31.1 1.0 CA A:ILE5 4.3 30.4 1.0 N A:ILE5 4.4 30.2 1.0 CB A:ILE5 4.4 33.5 1.0 N A:SER2 4.4 34.6 1.0 N A:VAL3 4.4 31.7 1.0 O A:HOH442 4.5 34.9 1.0 N A:ALA7 4.6 32.3 1.0 N A:GLY6 4.6 32.8 1.0 OG A:SER79 4.7 32.9 1.0 CA A:GLY6 4.7 33.8 1.0 CA A:VAL3 4.8 32.4 1.0 CE1 A:TYR80 4.9 33.5 1.0

Sodium binding site 2 out of 2 in the Structure of A Purine Nucleoside Phosphorylase From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Purine Nucleoside Phosphorylase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:33.2 occ:1.00 OG B:SER2 2.2 33.7 1.0 O B:ILE5 2.3 35.8 1.0 O B:HOH484 2.3 38.0 1.0 O B:SER2 2.5 31.4 1.0 OH B:TYR80 2.5 30.5 1.0 CB B:SER2 3.2 30.8 1.0 C B:SER2 3.4 30.5 1.0 C B:ILE5 3.5 33.8 1.0 CZ B:TYR80 3.5 33.8 1.0 O B:MET1 3.6 32.2 1.0 CA B:SER2 3.8 29.6 1.0 CE2 B:TYR80 3.8 29.4 1.0 O B:HOH417 3.9 35.9 1.0 CA B:ILE5 4.2 30.7 1.0 CB B:ILE5 4.2 29.3 1.0 O B:ALA7 4.3 31.4 1.0 N B:ILE5 4.3 31.8 1.0 C B:MET1 4.3 33.3 1.0 O B:HOH415 4.4 34.1 1.0 N B:SER2 4.5 33.0 1.0 N B:VAL3 4.5 28.8 1.0 N B:GLY6 4.6 33.1 1.0 N B:ALA7 4.6 33.4 1.0 OG B:SER79 4.7 33.3 1.0 CE1 B:TYR80 4.7 31.1 1.0 CA B:GLY6 4.7 32.8 1.0 CG2 B:ILE5 4.9 32.1 1.0 CA B:VAL3 4.9 30.7 1.0 C B:GLY6 4.9 37.5 1.0

F.M.Given, F.Moran, A.S.Johns, J.A.Titterington, T.M.Allison, D.L.Crittenden, J.M.Johnston. The Structure of His-Tagged Geobacillus Stearothermophilus Purine Nucleoside Phosphorylase Reveals A 'Spanner in the Works'. Acta Crystallogr.,Sect.F V. 78 416 2022.
ISSN: ESSN 2053-230X
PubMed: 36458621
DOI: 10.1107/S2053230X22011025