Sodium in PDB 5y4a: Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.

All present enzymatic activity of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.:
2.4.2.7;

The structure of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis., PDB code: 5y4a 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)	50.00 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.216, 77.547, 90.388, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.5

The structure of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. also contains other interesting chemical elements:

Cadmium

(Cd)

5 atoms

The binding sites of Sodium atom in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. (pdb code 5y4a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis., PDB code: 5y4a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:42.9 occ:1.00 O A:ILE120 2.3 29.4 1.0 O A:THR117 2.3 25.0 1.0 O A:HOH517 2.4 22.6 1.0 O A:HOH528 2.5 40.8 1.0 C A:THR117 3.5 25.9 1.0 C A:ILE120 3.5 30.1 1.0 CB A:GLN121 4.0 42.6 1.0 CA A:GLN121 4.1 38.2 1.0 CA A:ASP118 4.1 30.1 1.0 N A:GLN121 4.2 35.0 1.0 N A:ASP118 4.2 27.7 1.0 CD2 A:LEU149 4.3 26.7 1.0 C A:ASP118 4.3 29.7 1.0 N A:ILE120 4.4 26.3 1.0 O A:ASP118 4.4 32.4 1.0 CA A:THR117 4.5 24.7 1.0 CA A:ILE120 4.6 28.1 1.0 CB A:LEU149 4.6 26.9 1.0 O A:LEU149 4.7 32.0 1.0 N A:SER119 4.8 28.6 1.0 OD1 A:ASP118 4.9 40.7 1.0 CB A:THR117 4.9 25.5 1.0 CG A:LEU149 5.0 26.2 1.0 OE1 A:GLN121 5.0 57.1 1.0

Sodium binding site 2 out of 2 in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:33.0 occ:1.00 O B:HOH316 2.1 25.0 1.0 O B:ILE120 2.3 26.0 1.0 O B:HOH306 2.3 22.1 1.0 O B:THR117 2.4 25.9 1.0 O B:HOH317 2.6 40.7 1.0 C B:ILE120 3.6 27.3 1.0 C B:THR117 3.6 26.1 1.0 CA B:ASP118 4.3 28.9 1.0 CA B:GLN121 4.3 32.1 1.0 CD2 B:LEU149 4.3 30.4 1.0 N B:GLN121 4.3 29.1 1.0 N B:ASP118 4.4 26.7 1.0 O B:LEU149 4.4 32.2 1.0 CB B:LEU149 4.5 30.2 1.0 N B:ILE120 4.6 24.8 1.0 CA B:THR117 4.6 25.7 1.0 C B:ASP118 4.6 27.8 1.0 CA B:ILE120 4.7 25.9 1.0 CB B:THR117 4.9 26.8 1.0 CG B:LEU149 4.9 29.6 1.0 N B:SER119 4.9 25.3 1.0

G.C.Pavithra, U.A.Ramagopal. Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. To Be Published.