Atomistry » Sodium » PDB 4iic-4j0n » 4ip0
Atomistry »
  Sodium »
    PDB 4iic-4j0n »
      4ip0 »

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: Mon Oct 7 16:05:10 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy