Calcium in PDB 4nz1: Structure of Vibrio Cholerae Chitin De-N-Acetylase

All present enzymatic activity of Structure of Vibrio Cholerae Chitin De-N-Acetylase:
3.5.1.41;

The structure of Structure of Vibrio Cholerae Chitin De-N-Acetylase, PDB code: 4nz1 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)	29.05 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.394, 124.468, 62.244, 90.00, 111.00, 90.00
R / Rfree (%)	14.6 / 19.7

The structure of Structure of Vibrio Cholerae Chitin De-N-Acetylase also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Calcium atom in the Structure of Vibrio Cholerae Chitin De-N-Acetylase (pdb code 4nz1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Vibrio Cholerae Chitin De-N-Acetylase, PDB code: 4nz1:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Vibrio Cholerae Chitin De-N-Acetylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Vibrio Cholerae Chitin De-N-Acetylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:14.5 occ:1.00 O A:GLY355 2.3 14.4 1.0 O A:HOH604 2.3 19.7 1.0 O A:GLY223 2.3 13.7 1.0 O A:HOH601 2.4 12.0 1.0 O A:HOH603 2.5 18.5 1.0 O A:HOH602 2.5 15.1 1.0 C A:GLY223 3.4 15.1 1.0 C A:GLY355 3.4 14.3 1.0 CA A:GLY223 4.0 12.6 1.0 O A:HOH640 4.2 35.3 1.0 CA A:GLY355 4.2 21.9 1.0 OD1 A:ASP383 4.4 20.7 1.0 N A:VAL356 4.4 12.0 1.0 O A:HOH710 4.4 17.8 1.0 O A:HOH653 4.4 23.1 1.0 OD2 A:ASP383 4.5 18.9 1.0 CA A:VAL356 4.5 15.8 1.0 N A:TYR224 4.5 14.9 1.0 O A:HOH801 4.5 32.0 1.0 O A:HOH739 4.6 19.6 1.0 CG A:ASP383 4.8 24.9 1.0 CA A:TYR224 4.8 13.6 1.0 C A:TYR224 4.8 15.2 1.0 O A:GLU163 4.8 17.4 1.0 N A:GLN225 4.9 10.5 1.0 CG A:GLU163 4.9 23.6 1.0 CG A:GLN225 5.0 13.7 1.0

Calcium binding site 2 out of 3 in the Structure of Vibrio Cholerae Chitin De-N-Acetylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Vibrio Cholerae Chitin De-N-Acetylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:15.6 occ:1.00 O B:GLY355 2.2 16.3 1.0 O B:HOH601 2.3 16.0 1.0 O B:HOH602 2.3 14.0 1.0 O B:GLY223 2.4 13.8 1.0 O B:HOH604 2.4 13.8 1.0 O B:HOH603 2.5 16.9 1.0 C B:GLY355 3.4 21.6 1.0 C B:GLY223 3.5 17.1 1.0 CA B:GLY223 4.1 11.4 1.0 O B:HOH616 4.2 19.1 1.0 CA B:GLY355 4.3 17.8 1.0 O B:HOH783 4.3 16.3 1.0 N B:VAL356 4.4 16.5 1.0 O B:HOH634 4.4 22.1 1.0 CA B:VAL356 4.5 16.8 1.0 OD2 B:ASP383 4.5 19.0 1.0 OD1 B:ASP383 4.6 19.4 1.0 O B:HOH706 4.6 26.9 1.0 N B:TYR224 4.6 12.1 1.0 O B:HOH689 4.7 41.8 1.0 O B:GLU163 4.7 12.5 1.0 C B:TYR224 4.8 14.2 1.0 CA B:TYR224 4.8 10.8 1.0 N B:GLN225 4.9 16.1 1.0 CG B:GLU163 4.9 26.5 1.0 O B:HOH662 4.9 38.1 1.0 CG B:ASP383 4.9 25.1 1.0

Calcium binding site 3 out of 3 in the Structure of Vibrio Cholerae Chitin De-N-Acetylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Vibrio Cholerae Chitin De-N-Acetylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:27.5 occ:1.00 O1 B:EDO504 2.4 33.2 1.0 O2 A:EDO506 2.5 26.5 1.0 O A:HOH938 2.5 21.9 1.0 O A:HOH939 2.5 27.5 1.0 O1 A:EDO506 2.5 31.0 1.0 O A:HOH937 2.6 25.7 1.0 O B:HOH915 2.7 32.0 1.0 O2 B:EDO504 2.9 32.3 1.0 C1 B:EDO504 3.2 33.7 1.0 C1 A:EDO506 3.2 31.9 1.0 C2 A:EDO506 3.3 22.1 1.0 C2 B:EDO504 3.4 29.2 1.0 OE2 A:GLU140 4.4 24.7 1.0 OE1 B:GLU140 4.5 30.7 1.0 OE1 A:GLU140 4.6 31.0 1.0 NH2 A:ARG154 4.7 20.8 1.0 NH2 B:ARG154 4.7 30.2 1.0 OE2 B:GLU140 4.7 37.3 1.0 O A:HOH818 4.8 29.7 1.0 O B:HOH614 4.9 28.6 1.0 CD A:GLU140 4.9 28.0 1.0 O A:HOH936 4.9 26.6 1.0 O B:HOH864 5.0 29.2 1.0 CB B:TYR162 5.0 18.0 1.0 CD B:GLU140 5.0 26.4 1.0

E.Andres, D.Albesa-Jove, X.Biarnes, B.M.Moerschbacher, M.E.Guerin, A.Planas. Structural Basis of Chitin Oligosaccharide Deacetylation. Angew.Chem.Int.Ed.Engl. V. 53 6882 2014.
ISSN: ISSN 1433-7851
PubMed: 24810719
DOI: 10.1002/ANIE.201400220