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Sodium in PDB 4ip0: X-Ray Structure of the Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution

Enzymatic activity of X-Ray Structure of the Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution

All present enzymatic activity of X-Ray Structure of the Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure of the Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution, PDB code: 4ip0 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) 18.93 / 1.29
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.671, 71.062, 87.908, 69.63, 72.56, 85.73
R / Rfree (%) 17.2 / 20

Other elements in 4ip0:

The structure of X-Ray Structure of the Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution (pdb code 4ip0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of the Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution, PDB code: 4ip0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4ip0

Go back to Sodium Binding Sites List in 4ip0
Sodium binding site 1 out of 2 in the X-Ray Structure of the Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution


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 Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:5.5
occ:1.00
OE1 B:GLU48 2.9 8.2 1.0
O B:ILE68 2.9 6.0 1.0
OE2 A:GLU48 2.9 8.6 1.0
OG A:SER72 2.9 5.8 1.0
OG B:SER72 2.9 5.1 1.0
O A:ILE68 3.0 6.2 1.0
CB A:SER72 3.4 4.6 1.0
CB B:SER72 3.4 5.7 1.0
O B:HOH567 3.5 6.4 0.5
O B:HOH567 3.5 5.2 0.5
N A:ILE68 3.6 5.6 1.0
N B:ILE68 3.6 4.4 1.0
C B:ILE68 3.9 5.7 1.0
C A:ILE68 3.9 6.1 1.0
CD B:GLU48 3.9 8.2 1.0
CD A:GLU48 3.9 8.5 1.0
C A:GLY67 4.1 5.5 1.0
CA A:GLY67 4.1 6.5 1.0
CA B:GLY67 4.2 5.4 1.0
C B:GLY67 4.2 4.9 1.0
CA A:ILE68 4.2 6.2 1.0
CA B:ILE68 4.3 4.7 1.0
CG A:GLU48 4.3 8.1 1.0
CG B:GLU48 4.4 7.9 1.0
O B:THR66 4.7 6.3 1.0
CB A:ILE68 4.7 6.5 1.0
CA A:SER72 4.7 4.0 1.0
O A:THR66 4.7 6.5 1.0
CA B:SER72 4.7 4.5 1.0
CB B:ILE68 4.8 6.0 1.0
N A:SER72 4.8 4.1 1.0
N B:SER72 4.9 4.6 1.0
OE2 B:GLU48 4.9 9.1 1.0
CB B:GLU48 4.9 7.3 1.0
OE1 A:GLU48 4.9 9.7 1.0
N B:GLY69 5.0 5.9 1.0
CB A:GLU48 5.0 7.1 1.0

Sodium binding site 2 out of 2 in 4ip0

Go back to Sodium Binding Sites List in 4ip0
Sodium binding site 2 out of 2 in the X-Ray Structure of the Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution


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 Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:4.1
occ:1.00
OE2 E:GLU48 2.8 5.6 1.0
OE2 F:GLU48 2.9 6.6 1.0
O F:ILE68 2.9 4.5 1.0
OG F:SER72 2.9 3.7 1.0
OG E:SER72 2.9 3.7 1.0
O E:ILE68 2.9 5.2 1.0
CB E:SER72 3.4 3.7 1.0
CB F:SER72 3.4 4.2 1.0
O F:HOH506 3.4 5.5 0.4
O F:HOH506 3.5 3.7 0.6
N E:ILE68 3.6 4.2 1.0
N F:ILE68 3.7 3.2 1.0
C F:ILE68 3.8 3.8 1.0
CD F:GLU48 3.9 6.8 1.0
C E:ILE68 3.9 4.8 1.0
CD E:GLU48 3.9 5.9 1.0
CA E:GLY67 4.1 5.3 1.0
C E:GLY67 4.1 4.9 1.0
C F:GLY67 4.2 4.2 1.0
CA F:GLY67 4.3 4.6 1.0
CA E:ILE68 4.3 4.3 1.0
CG F:GLU48 4.3 6.4 1.0
CA F:ILE68 4.3 3.3 1.0
CG E:GLU48 4.4 6.1 1.0
O F:THR66 4.7 4.4 1.0
O E:THR66 4.7 5.4 1.0
CB E:ILE68 4.7 5.6 1.0
CA F:SER72 4.7 3.9 1.0
CA E:SER72 4.7 3.1 1.0
CB F:ILE68 4.8 4.3 1.0
OE1 F:GLU48 4.8 7.7 1.0
N F:SER72 4.9 3.8 1.0
N E:SER72 4.9 3.4 1.0
N F:GLY69 4.9 4.1 1.0
OE1 E:GLU48 4.9 7.5 1.0
CB F:GLU48 5.0 5.4 1.0
CB E:GLU48 5.0 6.0 1.0

Reference:

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure of the Complex Uridine Phosphorylase From Vibrio Cholerae with Phosphate Ion at 1.29 A Resolution To Be Published.
Page generated: Tue Dec 15 06:45:07 2020

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