Sodium in PDB 5efo: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A.

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A.:
2.4.2.3;

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A., PDB code: 5efo was solved by I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.63
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.949, 76.336, 89.694, 67.54, 73.74, 84.92
R / Rfree (%)	16.3 / 20.7

The binding sites of Sodium atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A. (pdb code 5efo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A., PDB code: 5efo:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:24.9 occ:1.00 OE2 A:GLU48 2.7 16.4 1.0 OE2 B:GLU48 2.7 17.9 1.0 OG B:SER72 2.9 13.7 1.0 O A:ILE68 2.9 13.0 1.0 O B:ILE68 3.0 11.7 1.0 OG A:SER72 3.0 12.3 1.0 CB B:SER72 3.4 12.3 1.0 CB A:SER72 3.5 11.8 1.0 N B:ILE68 3.5 11.5 1.0 N A:ILE68 3.6 13.1 1.0 O B:HOH420 3.7 23.2 1.0 CD A:GLU48 3.8 19.2 1.0 CD B:GLU48 3.8 18.3 1.0 C A:ILE68 3.9 12.4 1.0 C B:ILE68 3.9 10.3 1.0 C B:GLY67 4.1 13.0 1.0 CA B:GLY67 4.1 12.6 1.0 CA A:ILE68 4.2 13.2 1.0 C A:GLY67 4.2 12.1 1.0 CA B:ILE68 4.2 11.3 1.0 CA A:GLY67 4.2 12.6 1.0 CG B:GLU48 4.3 16.3 1.0 CG A:GLU48 4.3 21.3 1.0 CB A:ILE68 4.6 12.9 1.0 CB B:ILE68 4.7 11.2 1.0 CA B:SER72 4.7 10.3 1.0 O B:THR66 4.8 12.0 1.0 OE1 A:GLU48 4.8 19.0 1.0 CA A:SER72 4.8 9.7 1.0 OE1 B:GLU48 4.8 17.8 1.0 O A:THR66 4.9 12.7 1.0 N B:SER72 5.0 8.8 1.0

Sodium binding site 2 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na305 b:28.0 occ:1.00 OE2 D:GLU48 2.6 17.6 1.0 OE2 C:GLU48 2.7 16.0 1.0 OG D:SER72 2.7 13.4 1.0 O D:ILE68 2.9 12.1 1.0 O C:ILE68 2.9 12.1 1.0 OG C:SER72 3.1 13.1 1.0 CB D:SER72 3.3 12.8 1.0 CB C:SER72 3.5 13.2 1.0 N D:ILE68 3.6 12.3 1.0 N C:ILE68 3.6 14.2 1.0 O D:HOH433 3.6 18.0 0.7 O D:HOH433 3.7 5.7 0.3 CD D:GLU48 3.7 16.6 1.0 CD C:GLU48 3.8 18.6 1.0 C D:ILE68 3.9 12.9 1.0 C C:ILE68 3.9 10.3 1.0 C D:GLY67 4.1 11.7 1.0 CA D:GLY67 4.1 11.6 1.0 CA D:ILE68 4.2 12.3 1.0 CA C:ILE68 4.2 12.5 1.0 C C:GLY67 4.2 14.8 1.0 CG D:GLU48 4.2 18.6 1.0 CA C:GLY67 4.3 13.5 1.0 CG C:GLU48 4.4 17.6 1.0 CB C:ILE68 4.6 13.7 1.0 CA D:SER72 4.7 10.5 1.0 CB D:ILE68 4.7 13.9 1.0 O D:THR66 4.8 14.6 1.0 OE1 D:GLU48 4.8 18.0 1.0 OE1 C:GLU48 4.8 19.6 1.0 CA C:SER72 4.9 11.8 1.0 N D:SER72 4.9 9.4 1.0 O C:THR66 5.0 14.7 1.0

Sodium binding site 3 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.63A. within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:22.7 occ:1.00 OE2 F:GLU48 2.7 18.4 1.0 OE2 E:GLU48 2.7 15.1 1.0 OG E:SER72 2.8 11.5 1.0 OG F:SER72 2.9 13.2 1.0 O E:ILE68 2.9 11.9 1.0 O F:ILE68 3.0 11.1 1.0 CB E:SER72 3.4 11.0 1.0 CB F:SER72 3.4 13.1 1.0 N E:ILE68 3.5 12.1 1.0 O E:HOH450 3.5 6.0 0.4 N F:ILE68 3.6 12.4 1.0 O E:HOH450 3.7 12.7 0.6 CD E:GLU48 3.8 16.8 1.0 CD F:GLU48 3.8 18.2 1.0 C E:ILE68 3.9 11.2 1.0 C F:ILE68 3.9 11.1 1.0 CA E:GLY67 4.1 12.7 1.0 C E:GLY67 4.1 12.8 1.0 CA F:GLY67 4.2 11.5 1.0 CA E:ILE68 4.2 11.6 1.0 C F:GLY67 4.2 12.5 1.0 CA F:ILE68 4.3 10.8 1.0 CG E:GLU48 4.3 17.8 1.0 CG F:GLU48 4.4 18.0 1.0 CB E:ILE68 4.7 11.9 1.0 CB F:ILE68 4.7 12.4 1.0 CA E:SER72 4.7 9.9 1.0 CA F:SER72 4.8 11.4 1.0 O E:THR66 4.8 14.0 1.0 OE1 E:GLU48 4.8 17.3 1.0 OE1 F:GLU48 4.8 17.9 1.0 O F:THR66 4.8 13.9 1.0 N E:SER72 5.0 10.5 1.0 N F:SER72 5.0 10.6 1.0

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution To Be Published.