Zinc in PDB 4ny2: 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: 4ny2 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)	29.50 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.900, 112.540, 69.360, 90.00, 94.05, 90.00
R / Rfree (%)	14.7 / 18.5

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

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Structure of Vibrio Cholerae Chitin De-N-Acetylase (pdb code 4ny2). 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: 4ny2:
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:17.6 occ:1.00 OXT A:ACT503 2.0 14.1 1.0 NE2 A:HIS101 2.0 16.7 1.0 OD1 A:ASP40 2.1 14.2 1.0 NE2 A:HIS97 2.1 16.7 1.0 O A:ACT503 2.2 23.9 1.0 O A:HOH724 2.3 20.2 1.0 C A:ACT503 2.5 24.5 1.0 CD2 A:HIS101 3.0 17.8 1.0 CG A:ASP40 3.0 18.6 1.0 CD2 A:HIS97 3.1 16.4 1.0 CE1 A:HIS101 3.1 17.1 1.0 CE1 A:HIS97 3.2 15.5 1.0 OD2 A:ASP40 3.2 19.0 1.0 CB A:ASP39 4.0 16.9 1.0 CH3 A:ACT503 4.0 22.5 1.0 OD2 A:ASP39 4.0 20.4 1.0 CG A:HIS101 4.2 13.2 1.0 ND1 A:HIS101 4.2 19.6 1.0 NE2 A:HIS295 4.2 19.6 1.0 CG A:HIS97 4.2 13.0 1.0 ND1 A:HIS97 4.3 17.5 1.0 CB A:ASP40 4.4 16.8 1.0 CG A:ASP39 4.5 19.1 1.0 CD2 A:HIS295 4.5 24.1 1.0 CA A:PRO168 4.5 16.3 1.0 N A:ASP40 4.8 13.4 1.0 N A:TYR169 4.8 19.1 1.0 CA A:ASP40 4.9 13.5 1.0 CB A:PRO168 4.9 18.9 1.0 OD1 A:ASN65 4.9 16.9 1.0 C A:ASP39 5.0 16.4 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:20.4 occ:1.00 NE2 B:HIS101 2.0 21.5 1.0 OD1 B:ASP40 2.0 19.7 1.0 NE2 B:HIS97 2.2 15.8 1.0 O B:ACT503 2.2 24.2 1.0 OXT B:ACT503 2.2 21.6 1.0 O B:HOH801 2.4 26.9 1.0 C B:ACT503 2.6 24.5 1.0 CG B:ASP40 3.0 28.7 1.0 CD2 B:HIS101 3.0 22.2 1.0 CE1 B:HIS101 3.0 25.0 1.0 CD2 B:HIS97 3.1 15.0 1.0 CE1 B:HIS97 3.2 17.0 1.0 OD2 B:ASP40 3.2 24.2 1.0 CB B:ASP39 4.0 12.9 1.0 OD2 B:ASP39 4.0 20.9 1.0 CH3 B:ACT503 4.1 27.7 1.0 ND1 B:HIS101 4.1 18.8 1.0 CG B:HIS101 4.1 20.0 1.0 NE2 B:HIS295 4.2 27.1 1.0 ND1 B:HIS97 4.3 16.0 1.0 CG B:HIS97 4.3 13.1 1.0 CB B:ASP40 4.4 26.8 1.0 CD2 B:HIS295 4.5 22.8 1.0 CG B:ASP39 4.5 22.4 1.0 CA B:PRO168 4.5 20.3 1.0 N B:ASP40 4.8 20.1 1.0 CB B:PRO168 4.9 23.7 1.0 CA B:ASP40 4.9 19.6 1.0 N B:TYR169 4.9 19.2 1.0 OD1 B:ASN65 4.9 22.1 1.0 C B:ASP39 5.0 20.0 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