Sodium in PDB 6eyp: X-Ray Structure of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A

All present enzymatic activity of X-Ray Structure of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A:
2.4.2.3;

The structure of X-Ray Structure of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A, PDB code: 6eyp was solved by I.I.Prokofev, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.A.Lashkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.48 / 1.22
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	92.940, 92.940, 140.231, 90.00, 90.00, 120.00
R / Rfree (%)	13.8 / 17

The structure of X-Ray Structure of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A (pdb code 6eyp). 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 of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A, PDB code: 6eyp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Structure of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A


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 of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:9.6 occ:0.72 OE2 B:GLU48 2.7 12.5 1.0 OE2 A:GLU48 2.8 11.1 1.0 OG B:SER72 2.9 9.3 1.0 O A:ILE68 2.9 9.0 1.0 O B:ILE68 2.9 9.3 1.0 OG A:SER72 2.9 9.0 1.0 CB B:SER72 3.4 9.1 1.0 CB A:SER72 3.4 9.6 1.0 O A:HOH508 3.6 11.5 0.6 O A:HOH508 3.6 7.9 0.4 N B:ILE68 3.6 9.0 1.0 N A:ILE68 3.7 9.2 1.0 C B:ILE68 3.9 8.6 1.0 CD B:GLU48 3.9 12.0 1.0 CD A:GLU48 3.9 11.9 1.0 C A:ILE68 3.9 9.2 1.0 CA B:GLY67 4.1 9.4 1.0 CA A:GLY67 4.2 9.5 1.0 C B:GLY67 4.2 9.5 1.0 C A:GLY67 4.3 8.7 1.0 CA B:ILE68 4.3 8.8 1.0 CA A:ILE68 4.3 9.3 1.0 CG A:GLU48 4.4 11.6 1.0 CG B:GLU48 4.4 12.3 1.0 CB B:ILE68 4.7 9.6 1.0 CA B:SER72 4.7 8.0 1.0 CB A:ILE68 4.7 10.3 1.0 CA A:SER72 4.8 9.3 1.0 O A:THR66 4.8 10.1 1.0 O B:THR66 4.8 10.1 1.0 OE1 B:GLU48 4.9 13.9 1.0 OE1 A:GLU48 4.9 13.1 1.0 N B:SER72 4.9 8.1 1.0 N A:SER72 4.9 8.6 1.0

Sodium binding site 2 out of 3 in the X-Ray Structure of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A


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 of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:9.5 occ:0.77 OE2 C:GLU48 2.7 12.9 1.0 OE2 D:GLU48 2.7 12.8 1.0 O C:ILE68 2.8 9.7 1.0 O D:ILE68 2.9 9.2 1.0 OG C:SER72 2.9 9.9 1.0 OG D:SER72 2.9 9.2 1.0 CB C:SER72 3.4 9.4 1.0 CB D:SER72 3.4 9.6 1.0 O C:HOH512 3.5 9.0 0.6 O C:HOH512 3.5 7.7 0.4 N C:ILE68 3.6 9.0 1.0 N D:ILE68 3.7 8.9 1.0 C C:ILE68 3.8 8.8 1.0 CD C:GLU48 3.8 13.9 1.0 CD D:GLU48 3.9 13.0 1.0 C D:ILE68 3.9 9.0 1.0 CA C:GLY67 4.2 9.6 1.0 C C:GLY67 4.2 9.0 1.0 CA D:GLY67 4.2 9.9 1.0 C D:GLY67 4.2 8.7 1.0 CA C:ILE68 4.2 8.8 1.0 CA D:ILE68 4.3 9.8 1.0 CG C:GLU48 4.4 13.0 1.0 CG D:GLU48 4.4 14.4 1.0 CB D:ILE68 4.7 9.9 1.0 CB C:ILE68 4.7 10.2 1.0 CA C:SER72 4.7 7.7 1.0 CA D:SER72 4.8 8.0 1.0 OE1 C:GLU48 4.9 14.4 1.0 OE1 D:GLU48 4.9 14.7 1.0 O C:THR66 4.9 10.1 1.0 O D:THR66 4.9 10.7 1.0 N D:SER72 4.9 7.5 1.0 N C:SER72 4.9 7.9 1.0 N C:GLY69 5.0 8.9 1.0

Sodium binding site 3 out of 3 in the X-Ray Structure of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A


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 of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A within 5.0Å range: probe atom residue distance (Å) B Occ E:Na302 b:14.0 occ:0.94 OE2 F:GLU48 2.8 14.0 1.0 OE2 E:GLU48 2.8 13.8 1.0 OG F:SER72 2.8 11.1 1.0 O E:ILE68 2.8 10.7 1.0 O F:ILE68 2.9 10.6 1.0 OG E:SER72 2.9 10.9 1.0 CB F:SER72 3.4 11.0 1.0 CB E:SER72 3.4 10.7 1.0 O E:HOH467 3.5 10.4 0.5 O E:HOH467 3.5 10.1 0.5 N E:ILE68 3.6 10.4 1.0 N F:ILE68 3.7 10.2 1.0 C E:ILE68 3.8 10.0 1.0 C F:ILE68 3.9 9.8 1.0 CD F:GLU48 3.9 14.3 1.0 CD E:GLU48 3.9 14.1 1.0 CA E:GLY67 4.2 10.6 1.0 C E:GLY67 4.2 10.4 1.0 CA E:ILE68 4.2 9.9 1.0 CA F:GLY67 4.2 11.9 1.0 C F:GLY67 4.3 10.9 1.0 CA F:ILE68 4.3 9.8 1.0 CG F:GLU48 4.4 14.0 1.0 CG E:GLU48 4.5 14.2 1.0 CB E:ILE68 4.7 11.1 1.0 CA F:SER72 4.7 10.4 1.0 CB F:ILE68 4.7 10.4 1.0 CA E:SER72 4.7 9.2 1.0 N F:SER72 4.9 9.7 1.0 O F:THR66 4.9 11.8 1.0 OE1 F:GLU48 4.9 15.3 1.0 O E:THR66 4.9 11.8 1.0 N E:SER72 4.9 9.6 1.0 OE1 E:GLU48 4.9 14.6 1.0 N E:GLY69 5.0 9.9 1.0

I.I.Prokofev, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.A.Lashkov. X-Ray Structure of the Unliganded Uridine Phosphorylase From Vibrio Cholerae at 1.22A To Be Published.