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Sodium in PDB 4nz5: Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion

Enzymatic activity of Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion

All present enzymatic activity of Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion:
3.5.1.41;

Protein crystallography data

The structure of Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion, PDB code: 4nz5 was solved by D.Albesa-Jove, E.Andres, X.Biarnes, A.Planas, M.E.Guerin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.44 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.664, 112.525, 69.815, 90.00, 94.35, 90.00
R / Rfree (%) 16.8 / 20.1

Other elements in 4nz5:

The structure of Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion (pdb code 4nz5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion, PDB code: 4nz5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4nz5

Go back to Sodium Binding Sites List in 4nz5
Sodium binding site 1 out of 2 in the Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:14.8
occ:1.00
 O A:GLY355 2.1 18.5 1.0
O A:HOH603 2.3 22.7 1.0
O A:GLY223 2.3 11.7 1.0
O A:HOH602 2.3 18.3 1.0
O A:HOH601 2.3 21.4 1.0
O A:HOH604 2.4 16.9 1.0
C A:GLY355 3.3 20.2 1.0
C A:GLY223 3.4 12.8 1.0
CA A:GLY223 3.9 14.3 1.0
CA A:GLY355 4.0 25.0 1.0
O A:HOH856 4.1 42.1 1.0
N A:VAL356 4.3 17.8 1.0
O A:HOH839 4.3 37.3 1.0
O A:HOH616 4.3 14.1 1.0
O A:HOH639 4.4 22.9 1.0
OD2 A:ASP383 4.5 18.4 1.0
CA A:VAL356 4.5 11.5 1.0
N A:TYR224 4.5 10.8 1.0
OD1 A:ASP383 4.5 14.7 1.0
O A:HOH644 4.5 15.1 1.0
CG A:GLU163 4.8 22.2 1.0
C A:TYR224 4.8 12.9 1.0
CA A:TYR224 4.8 10.2 1.0
O A:GLU163 4.8 11.9 1.0
CG A:ASP383 4.8 19.3 1.0
N A:GLN225 4.9 9.6 1.0

Sodium binding site 2 out of 2 in 4nz5

Go back to Sodium Binding Sites List in 4nz5
Sodium binding site 2 out of 2 in the Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Vibrio Cholerae Chitin De-N-Acetylase in Complex with 2- (Acetylamino)-2-Deoxy-A-D-Glucopyranose (Ndg) and Cadmium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:10.3
occ:1.00
 O B:GLY223 2.1 11.1 1.0
O B:GLY355 2.2 14.4 1.0
O B:HOH602 2.2 15.9 1.0
O B:HOH601 2.2 24.1 1.0
O B:HOH751 2.3 17.8 1.0
O B:HOH603 2.3 17.7 1.0
C B:GLY223 3.2 14.4 1.0
C B:GLY355 3.4 20.4 1.0
CA B:GLY223 3.8 13.0 1.0
CA B:GLY355 4.2 15.8 1.0
O B:HOH638 4.2 19.1 1.0
O B:HOH752 4.3 31.9 1.0
O B:HOH616 4.3 9.9 1.0
N B:TYR224 4.3 9.9 1.0
N B:VAL356 4.3 12.2 1.0
O B:HOH723 4.5 25.7 1.0
O B:HOH627 4.5 19.2 1.0
OD2 B:ASP383 4.5 15.4 1.0
OD1 B:ASP383 4.5 13.6 1.0
CA B:VAL356 4.5 13.2 1.0
CA B:TYR224 4.6 10.3 1.0
C B:TYR224 4.6 10.2 1.0
O B:GLU163 4.7 11.7 1.0
N B:GLN225 4.8 8.9 1.0
CG B:GLU163 4.8 21.9 1.0
CG B:ASP383 4.8 19.4 1.0

Reference:

E.Andres, D.Albesa-Jove, X.Biarnes, B.M.Moerschbacher, M.E.Guerin, A.Planas. Vibrio Cholerae Protein To Be Published.
Page generated: Mon Oct 7 17:20:00 2024

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