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Cadmium 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:

Sodium (Na) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 2 binding sites of Cadmium 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 Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 4nz5

Go back to Cadmium Binding Sites List in 4nz5
Cadmium 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 Cadmium with other atoms in the Cd 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:Cd502

b:19.1
occ:1.00
 NE2 A:HIS101 2.3 15.2 1.0
O A:HOH605 2.4 17.0 1.0
OD1 A:ASP40 2.4 18.2 1.0
OXT A:ACT503 2.4 11.8 1.0
NE2 A:HIS97 2.4 16.6 1.0
O A:ACT503 2.5 16.9 1.0
C A:ACT503 2.8 21.1 1.0
CG A:ASP40 3.2 17.4 1.0
OD2 A:ASP40 3.3 18.2 1.0
CD2 A:HIS101 3.3 21.0 1.0
CD2 A:HIS97 3.3 12.3 1.0
CE1 A:HIS101 3.3 20.7 1.0
CE1 A:HIS97 3.5 15.6 1.0
CB A:ASP39 4.0 14.7 1.0
NE2 A:HIS295 4.1 19.8 1.0
OD2 A:ASP39 4.2 17.0 1.0
CH3 A:ACT503 4.3 15.5 1.0
CD2 A:HIS295 4.4 16.0 1.0
CG A:HIS101 4.4 14.9 1.0
ND1 A:HIS101 4.4 17.1 1.0
CG A:HIS97 4.5 19.3 1.0
ND1 A:HIS97 4.6 16.9 1.0
CG A:ASP39 4.6 17.1 1.0
CA A:PRO168 4.6 17.8 1.0
CB A:ASP40 4.6 17.4 1.0
N A:TYR169 4.8 18.3 1.0
N A:ASP40 4.9 13.3 1.0
CB A:PRO168 5.0 16.4 1.0
O A:NDG504 5.0 43.9 1.0

Cadmium binding site 2 out of 2 in 4nz5

Go back to Cadmium Binding Sites List in 4nz5
Cadmium 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 Cadmium with other atoms in the Cd 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:Cd502

b:20.0
occ:1.00
 O B:HOH604 2.1 18.9 1.0
OD1 B:ASP40 2.4 18.5 1.0
NE2 B:HIS101 2.4 21.5 1.0
NE2 B:HIS97 2.4 11.5 1.0
O B:ACT503 2.4 19.0 1.0
OXT B:ACT503 2.4 18.0 1.0
C B:ACT503 2.8 19.6 1.0
CG B:ASP40 3.1 23.8 1.0
OD2 B:ASP40 3.1 18.9 1.0
CD2 B:HIS101 3.2 18.0 1.0
CD2 B:HIS97 3.3 14.9 1.0
CE1 B:HIS97 3.5 14.4 1.0
CE1 B:HIS101 3.5 20.6 1.0
NE2 B:HIS295 4.0 23.3 1.0
CB B:ASP39 4.1 12.7 1.0
O B:HOH637 4.3 38.7 1.0
OD2 B:ASP39 4.3 15.6 1.0
CH3 B:ACT503 4.3 18.1 1.0
CD2 B:HIS295 4.4 14.3 1.0
CG B:HIS101 4.5 17.7 1.0
CG B:HIS97 4.5 10.8 1.0
ND1 B:HIS101 4.5 20.6 1.0
ND1 B:HIS97 4.5 15.5 1.0
CB B:ASP40 4.6 18.0 1.0
CA B:PRO168 4.6 18.1 1.0
CG B:ASP39 4.7 16.9 1.0
N B:TYR169 4.8 18.6 1.0
O2 B:GOL506 4.8 47.4 1.0
N B:ASP40 4.9 16.7 1.0
C B:ASP39 5.0 18.1 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: Sat Dec 12 08:25:21 2020

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