Zinc in PDB 4nz3: 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: 4nz3 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)	29.71 / 2.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.684, 98.142, 152.988, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 21.3

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Structure of Vibrio Cholerae Chitin De-N-Acetylase (pdb code 4nz3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Vibrio Cholerae Chitin De-N-Acetylase, PDB code: 4nz3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Vibrio Cholerae Chitin De-N-Acetylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn501 b:15.9 occ:1.00 O A:HOH1071 1.9 41.4 1.0 NE2 A:HIS101 2.0 14.4 1.0 O7 A:NAG504 2.1 26.3 1.0 OD1 A:ASP40 2.2 13.8 1.0 NE2 A:HIS97 2.2 7.1 1.0 O3 A:NAG504 2.6 21.6 1.0 C7 A:NAG504 2.8 33.1 1.0 CD2 A:HIS101 2.9 16.0 1.0 CE1 A:HIS101 3.0 9.8 1.0 CG A:ASP40 3.1 18.7 1.0 CD2 A:HIS97 3.1 9.3 1.0 CE1 A:HIS97 3.3 12.5 1.0 OD2 A:ASP40 3.3 11.5 1.0 C8 A:NAG504 3.5 30.9 1.0 N2 A:NAG504 3.6 39.1 1.0 C3 A:NAG504 3.8 30.4 1.0 C2 A:NAG504 4.0 25.3 1.0 CB A:SER39 4.0 9.9 1.0 NE2 A:HIS295 4.1 18.4 1.0 CG A:HIS101 4.1 10.7 1.0 ND1 A:HIS101 4.1 15.7 1.0 CG A:HIS97 4.3 7.7 1.0 ND1 A:HIS97 4.3 11.3 1.0 CD2 A:HIS295 4.4 13.5 1.0 CA A:PRO168 4.4 9.0 1.0 CB A:ASP40 4.4 13.2 1.0 OG A:SER39 4.6 24.1 1.0 N A:ASP40 4.7 13.2 1.0 N A:TYR169 4.7 9.3 1.0 CB A:PRO168 4.8 10.9 1.0 CA A:ASP40 4.8 13.6 1.0 OD1 A:ASN65 4.9 12.9 1.0 C4 A:NAG504 4.9 20.5 1.0 C A:SER39 5.0 15.2 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn501 b:14.0 occ:1.00 O B:HOH976 1.7 42.8 1.0 NE2 B:HIS101 2.0 10.4 1.0 OD1 B:ASP40 2.2 6.7 1.0 NE2 B:HIS97 2.2 10.2 1.0 O7 B:NAG504 2.3 17.5 1.0 C7 B:NAG504 2.6 34.7 1.0 O3 B:NAG504 2.7 29.0 1.0 CD2 B:HIS101 2.9 10.2 1.0 CE1 B:HIS101 3.0 7.8 1.0 C8 B:NAG504 3.0 30.0 1.0 CD2 B:HIS97 3.1 9.2 1.0 CG B:ASP40 3.1 14.6 1.0 CE1 B:HIS97 3.3 13.8 1.0 N2 B:NAG504 3.3 41.1 1.0 OD2 B:ASP40 3.4 16.6 1.0 C3 B:NAG504 3.8 34.5 1.0 C2 B:NAG504 3.9 33.4 1.0 CB B:SER39 3.9 11.4 1.0 CG B:HIS101 4.0 11.5 1.0 ND1 B:HIS101 4.1 7.8 1.0 NE2 B:HIS295 4.2 13.7 1.0 CG B:HIS97 4.3 9.9 1.0 ND1 B:HIS97 4.4 15.3 1.0 CA B:PRO168 4.4 9.8 1.0 CD2 B:HIS295 4.5 12.8 1.0 OG B:SER39 4.5 21.6 1.0 CB B:ASP40 4.5 14.0 1.0 N B:ASP40 4.7 10.2 1.0 N B:TYR169 4.7 13.1 1.0 CA B:ASP40 4.9 8.0 1.0 CB B:PRO168 4.9 16.3 1.0 OD1 B:ASN65 5.0 9.5 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