Sodium in PDB 5y07: Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp.

All present enzymatic activity of Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp.:
2.4.2.7;

The structure of Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp., PDB code: 5y07 was solved by G.C.Pavithra, U.A.Ramagopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.70 / 2.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.301, 86.292, 48.553, 90.00, 105.87, 90.00
R / Rfree (%)	18.7 / 23.5

The structure of Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp. also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp. (pdb code 5y07). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp., PDB code: 5y07:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:32.2 occ:1.00 O A:HOH336 2.0 29.6 1.0 O A:ILE120 2.3 21.2 1.0 O A:THR117 2.4 20.6 1.0 O A:HOH307 2.5 22.9 1.0 C A:ILE120 3.5 22.7 1.0 C A:THR117 3.5 20.0 1.0 CA A:GLN121 4.1 28.3 1.0 CB A:GLN121 4.2 31.6 1.0 N A:GLN121 4.2 25.2 1.0 CA A:ASP118 4.2 24.6 1.0 N A:ASP118 4.3 21.7 1.0 C A:ASP118 4.4 23.3 1.0 N A:ILE120 4.4 19.8 1.0 CB A:LEU149 4.5 20.9 1.0 O A:LEU149 4.5 22.2 1.0 CA A:ILE120 4.5 21.2 1.0 CA A:THR117 4.5 18.6 1.0 CD2 A:LEU149 4.6 21.9 1.0 O A:ASP118 4.6 23.3 1.0 N A:SER119 4.8 22.2 1.0 CB A:THR117 4.9 18.4 1.0 CG A:LEU149 4.9 21.1 1.0 CD1 A:LEU149 4.9 19.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:32.3 occ:1.00 O B:HOH335 2.1 25.9 1.0 O B:HOH334 2.3 31.0 1.0 O B:ILE120 2.3 23.8 1.0 O B:HOH304 2.4 28.3 1.0 O B:THR117 2.4 21.6 1.0 C B:ILE120 3.5 24.0 1.0 C B:THR117 3.5 20.1 1.0 CA B:ASP118 4.1 22.2 1.0 CA B:GLN121 4.1 27.6 1.0 N B:GLN121 4.3 25.2 1.0 N B:ASP118 4.3 21.2 1.0 C B:ASP118 4.4 21.3 1.0 O B:LEU149 4.4 22.2 1.0 N B:ILE120 4.4 21.5 1.0 CD2 B:LEU149 4.4 22.3 1.0 CB B:LEU149 4.5 20.8 1.0 CA B:THR117 4.5 19.4 1.0 CA B:ILE120 4.6 22.6 1.0 CB B:GLN121 4.6 31.4 1.0 O B:ASP118 4.8 19.5 1.0 N B:SER119 4.8 19.7 1.0 CG B:LEU149 4.9 21.4 1.0 CB B:THR117 4.9 19.8 1.0

U.A.Ramagopal, G.C.Pavithra. Crystal Structure of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis with Prpp To Be Published.