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Sodium in PDB 5miw: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.

Enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A., PDB code: 5miw was solved by I.I.Prokofev, A.A.Lashkov, V.V.Balaev, 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) 32.03 / 1.28
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.513, 71.948, 89.332, 69.22, 72.20, 85.60
R / Rfree (%) 13.2 / 16.9

Other elements in 5miw:

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. (pdb code 5miw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A., PDB code: 5miw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5miw

Go back to Sodium Binding Sites List in 5miw
Sodium binding site 1 out of 6 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


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 Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:12.2
occ:0.59
 OE2 A:GLU48 2.6 14.8 1.0
OE2 B:GLU48 2.7 15.2 1.0
OG A:SER72 2.8 7.8 0.7
OG B:SER72 2.9 7.1 0.7
O B:ILE68 2.9 8.2 1.0
O A:ILE68 2.9 7.3 1.0
CB A:SER72 3.1 5.5 0.3
CB B:SER72 3.2 8.4 0.3
OG A:SER72 3.3 4.9 0.3
CB A:SER72 3.3 8.1 0.7
CB B:SER72 3.3 7.8 0.7
OG B:SER72 3.4 9.2 0.3
N B:ILE68 3.5 9.0 1.0
N A:ILE68 3.6 8.4 1.0
O A:HOH491 3.6 5.7 0.4
O A:HOH491 3.7 10.7 0.6
CD A:GLU48 3.8 15.2 1.0
C B:ILE68 3.9 7.1 1.0
CD B:GLU48 3.9 16.3 1.0
C A:ILE68 3.9 7.1 1.0
CA B:GLY67 4.1 9.7 1.0
C B:GLY67 4.1 8.7 1.0
CA A:GLY67 4.2 9.3 1.0
CA B:ILE68 4.2 7.8 1.0
C A:GLY67 4.2 8.4 1.0
CA A:ILE68 4.3 7.2 1.0
CG A:GLU48 4.4 15.9 1.0
CG B:GLU48 4.4 16.4 1.0
CA A:SER72 4.5 6.1 0.3
CB B:ILE68 4.6 9.1 1.0
CA B:SER72 4.6 7.7 0.3
CA A:SER72 4.7 6.9 0.7
CA B:SER72 4.7 7.7 0.7
CB A:ILE68 4.7 9.2 1.0
O B:THR66 4.8 10.3 1.0
O A:THR66 4.8 9.9 1.0
OE1 A:GLU48 4.8 15.8 1.0
OE1 B:GLU48 4.8 16.1 1.0
N A:SER72 4.9 7.0 0.7
N A:SER72 4.9 6.4 0.3
N B:SER72 4.9 7.9 1.0

Sodium binding site 2 out of 6 in 5miw

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Sodium binding site 2 out of 6 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


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 Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:19.5
occ:1.00
 O F:HOH683 2.7 15.2 1.0
O A:HOH703 2.8 17.9 1.0
OG1 A:THR137 2.8 9.9 1.0
OG1 F:THR137 2.8 11.0 1.0
CZ A:PHE133 3.5 12.0 1.0
CG2 A:THR137 3.5 10.9 1.0
CE2 F:PHE133 3.5 12.8 1.0
CE2 A:PHE133 3.5 12.3 1.0
CG2 F:THR137 3.5 10.7 1.0
CZ F:PHE133 3.5 12.7 1.0
CB F:THR137 3.7 10.0 1.0
CB A:THR137 3.7 9.3 1.0
CA A:THR137 4.4 8.9 1.0
CA F:THR137 4.4 9.4 1.0
CD2 F:PHE133 4.5 11.2 1.0
CE1 A:PHE133 4.5 11.8 1.0
CD2 A:PHE133 4.5 11.6 1.0
O F:HOH727 4.5 36.6 1.0
O A:HOH746 4.5 35.8 1.0
O A:HOH564 4.6 13.7 1.0
O A:HOH525 4.6 31.6 1.0
CE1 F:PHE133 4.6 12.2 1.0
O F:HOH563 4.7 15.2 1.0
O F:HOH583 4.7 23.5 1.0

Sodium binding site 3 out of 6 in 5miw

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Sodium binding site 3 out of 6 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


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 Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na307

b:18.2
occ:1.00
 O C:HOH658 2.7 15.5 1.0
O B:HOH668 2.7 16.4 1.0
OG1 C:THR137 2.8 11.2 1.0
OG1 B:THR137 2.8 11.1 1.0
CZ C:PHE133 3.5 13.9 1.0
CE2 B:PHE133 3.5 13.3 1.0
CG2 C:THR137 3.5 12.1 1.0
CG2 B:THR137 3.5 11.6 1.0
CE2 C:PHE133 3.6 13.4 1.0
CZ B:PHE133 3.6 13.9 1.0
CB C:THR137 3.7 10.1 1.0
CB B:THR137 3.7 10.9 1.0
O C:HOH694 4.3 29.6 1.0
CA C:THR137 4.4 9.3 1.0
CE1 C:PHE133 4.4 14.7 1.0
CA B:THR137 4.4 10.2 1.0
CD2 B:PHE133 4.5 11.6 1.0
O B:HOH711 4.5 36.9 1.0
CD2 C:PHE133 4.6 12.1 1.0
CE1 B:PHE133 4.7 13.5 1.0
O B:HOH538 4.7 23.7 1.0
O C:HOH546 4.7 28.9 1.0
O C:HOH525 4.7 14.9 1.0
O B:HOH562 4.7 14.2 1.0

Sodium binding site 4 out of 6 in 5miw

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Sodium binding site 4 out of 6 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na307

b:12.9
occ:0.67
 OE2 C:GLU48 2.7 15.1 1.0
OE2 D:GLU48 2.7 12.7 1.0
OG C:SER72 2.9 11.1 1.0
O D:ILE68 2.9 9.1 1.0
O C:ILE68 2.9 8.9 1.0
OG D:SER72 3.0 8.0 0.8
CB D:SER72 3.2 6.9 0.2
CB C:SER72 3.3 10.7 1.0
OG D:SER72 3.4 6.7 0.2
CB D:SER72 3.4 8.9 0.8
N C:ILE68 3.6 8.4 1.0
N D:ILE68 3.6 9.5 1.0
O D:HOH482 3.6 7.7 0.5
O D:HOH482 3.6 11.6 0.5
CD C:GLU48 3.8 15.6 1.0
CD D:GLU48 3.8 15.0 1.0
C C:ILE68 3.9 7.4 1.0
C D:ILE68 3.9 8.4 1.0
CA C:GLY67 4.2 10.7 1.0
C C:GLY67 4.2 9.6 1.0
CA D:GLY67 4.2 10.7 1.0
C D:GLY67 4.2 10.6 1.0
CA D:ILE68 4.2 8.4 1.0
CA C:ILE68 4.2 9.4 1.0
CG D:GLU48 4.4 15.5 1.0
CG C:GLU48 4.4 15.8 1.0
CA D:SER72 4.6 7.1 0.2
CB D:ILE68 4.7 9.7 1.0
CA C:SER72 4.7 8.2 1.0
CB C:ILE68 4.7 10.8 1.0
CA D:SER72 4.8 7.9 0.8
OE1 D:GLU48 4.8 15.1 1.0
O C:THR66 4.8 10.2 1.0
OE1 C:GLU48 4.8 15.8 1.0
O D:THR66 4.9 11.8 1.0
N C:SER72 4.9 7.8 1.0
N D:SER72 4.9 7.3 0.2
N D:SER72 5.0 7.7 0.8

Sodium binding site 5 out of 6 in 5miw

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Sodium binding site 5 out of 6 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:21.1
occ:1.00
 OG1 D:THR137 2.7 12.7 1.0
O D:HOH649 2.7 19.0 1.0
O E:HOH677 2.8 17.6 1.0
OG1 E:THR137 2.8 13.0 1.0
CE2 D:PHE133 3.4 15.8 1.0
CZ E:PHE133 3.5 16.1 1.0
CG2 E:THR137 3.5 11.8 1.0
CZ D:PHE133 3.5 16.2 1.0
CE2 E:PHE133 3.6 15.9 1.0
CG2 D:THR137 3.6 15.1 1.0
CB D:THR137 3.7 13.5 1.0
CB E:THR137 3.7 12.0 1.0
O E:HOH713 4.4 34.7 1.0
CA D:THR137 4.4 12.3 1.0
CA E:THR137 4.4 11.0 1.0
CD2 D:PHE133 4.5 14.9 1.0
CE1 E:PHE133 4.5 16.1 1.0
O D:HOH686 4.6 45.6 1.0
CE1 D:PHE133 4.6 15.7 1.0
CD2 E:PHE133 4.6 14.8 1.0
O E:HOH573 4.7 17.5 1.0
O E:HOH447 4.7 35.7 1.0
O D:HOH539 4.7 18.3 1.0
O D:HOH445 4.7 25.8 1.0

Sodium binding site 6 out of 6 in 5miw

Go back to Sodium Binding Sites List in 5miw
Sodium binding site 6 out of 6 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:10.4
occ:0.63
 OE2 E:GLU48 2.7 12.8 1.0
OE2 F:GLU48 2.7 12.1 1.0
OG E:SER72 2.9 7.5 0.8
OG F:SER72 2.9 7.3 0.8
O F:ILE68 2.9 7.5 1.0
O E:ILE68 3.0 8.6 1.0
CB E:SER72 3.1 6.4 0.2
CB F:SER72 3.2 6.3 0.2
OG E:SER72 3.3 6.1 0.2
CB E:SER72 3.3 8.1 0.8
CB F:SER72 3.4 7.8 0.8
OG F:SER72 3.4 6.4 0.2
N E:ILE68 3.6 8.2 1.0
O F:HOH455 3.6 8.3 0.5
N F:ILE68 3.6 8.1 1.0
O F:HOH455 3.6 10.1 0.5
CD E:GLU48 3.8 13.6 1.0
C F:ILE68 3.9 7.0 1.0
CD F:GLU48 3.9 12.7 1.0
C E:ILE68 3.9 6.7 1.0
CA E:GLY67 4.1 8.0 1.0
C E:GLY67 4.2 7.9 1.0
C F:GLY67 4.2 8.4 1.0
CA F:GLY67 4.2 8.4 1.0
CA F:ILE68 4.2 7.2 1.0
CA E:ILE68 4.2 6.8 1.0
CG E:GLU48 4.4 12.9 1.0
CG F:GLU48 4.5 12.9 1.0
CA E:SER72 4.5 6.4 0.2
CA F:SER72 4.6 6.2 0.2
CB F:ILE68 4.7 8.2 1.0
CA E:SER72 4.7 7.4 0.8
CB E:ILE68 4.7 8.3 1.0
CA F:SER72 4.7 6.7 0.8
O E:THR66 4.8 8.6 1.0
OE1 E:GLU48 4.8 14.2 1.0
O F:THR66 4.8 9.1 1.0
OE1 F:GLU48 4.9 14.1 1.0
N E:SER72 4.9 6.3 0.8
N F:SER72 4.9 7.2 0.8
N E:SER72 4.9 6.1 0.2
N F:SER72 4.9 6.3 0.2

Reference:

I.I.Prokofev, A.A.Lashkov, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. To Be Published.
Page generated: Tue Dec 15 11:18:39 2020

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