Sodium in PDB 8w7h: Purine Nucleoside Phosphorylase in Complex with MMV000848

The structure of Purine Nucleoside Phosphorylase in Complex with MMV000848, PDB code: 8w7h was solved by Z.Chung, J.Q.Lin, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.17 / 1.85
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	95.61, 95.61, 138.2, 90, 90, 120
R / Rfree (%)	17.3 / 17.7

The binding sites of Sodium atom in the Purine Nucleoside Phosphorylase in Complex with MMV000848 (pdb code 8w7h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Purine Nucleoside Phosphorylase in Complex with MMV000848, PDB code: 8w7h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Purine Nucleoside Phosphorylase in Complex with MMV000848


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Purine Nucleoside Phosphorylase in Complex with MMV000848 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:28.8 occ:0.50 O A:HOH440 2.7 39.1 1.0 OE1 A:GLU46 2.7 35.4 1.0 O A:VAL66 2.8 28.6 1.0 N A:VAL66 3.4 31.4 1.0 C A:VAL66 3.7 26.8 1.0 O A:HOH476 3.8 27.6 0.5 CD A:GLU46 3.9 35.6 1.0 CA A:VAL66 4.1 29.8 1.0 C A:GLY65 4.1 34.1 1.0 CA A:GLY65 4.2 25.4 1.0 CA A:GLY70 4.3 24.3 1.0 CB A:VAL66 4.5 33.9 1.0 CG A:GLU46 4.5 33.8 1.0 N A:GLY67 4.9 31.6 1.0 OE2 A:GLU46 4.9 37.0 1.0 O A:HIS64 5.0 30.5 1.0 N A:GLY70 5.0 26.0 1.0

Sodium binding site 2 out of 2 in the Purine Nucleoside Phosphorylase in Complex with MMV000848


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Purine Nucleoside Phosphorylase in Complex with MMV000848 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:32.0 occ:0.50 OG A:SER68 2.9 26.8 1.0 N A:ALA69 3.1 24.4 1.0 OD2 A:ASP158 3.1 25.8 1.0 CB A:ALA69 3.3 24.8 1.0 O A:HOH414 3.4 24.9 1.0 CG A:ASP158 3.8 27.0 1.0 CA A:ALA69 3.8 24.9 1.0 N A:SER68 3.9 24.8 1.0 C A:SER68 4.1 24.5 1.0 CB A:SER68 4.1 26.2 1.0 O A:HOH476 4.2 27.6 0.5 OD1 A:ASP158 4.2 26.7 1.0 CA A:SER68 4.2 26.5 1.0 CB A:ASP158 4.7 24.1 1.0 C A:GLY67 4.7 29.7 1.0 O A:HOH412 4.7 26.0 1.0 C A:ALA69 5.0 28.2 1.0

Z.Chung, J.Lin, G.Wirjanata, J.M.Dziekan, A.El Sahili, P.R.Preiser, Z.Bozdech, J.Lescar. Identification and Structural Validation of Purine Nucleoside Phosphorylase From Plasmodium Falciparum As A Target of MMV00848. J.Biol.Chem. 05586 2023.
ISSN: ESSN 1083-351X
PubMed: 38141766
DOI: 10.1016/J.JBC.2023.105586