Zinc in PDB 4nyy: 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: 4nyy 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)	49.15 / 2.65
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.170, 165.010, 203.360, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 22.7

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

Sodium

(Na)

4 atoms

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

Zinc binding site 1 out of 4 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:68.8 occ:1.00 NE2 A:HIS101 2.1 11.6 1.0 OD1 A:ASP40 2.1 23.9 1.0 OXT A:ACT503 2.3 25.8 1.0 O A:ACT503 2.5 25.8 1.0 NE2 A:HIS97 2.6 2.4 1.0 C A:ACT503 2.8 25.8 1.0 CE1 A:HIS101 3.0 11.6 1.0 CG A:ASP40 3.0 23.9 1.0 CD2 A:HIS101 3.0 11.6 1.0 OD2 A:ASP40 3.2 23.9 1.0 O A:HOH601 3.2 14.3 1.0 CE1 A:HIS97 3.5 2.4 1.0 CD2 A:HIS97 3.5 2.4 1.0 NE2 A:HIS295 4.0 10.5 1.0 ND1 A:HIS101 4.1 11.6 1.0 CB A:ASP39 4.1 7.5 1.0 CG A:HIS101 4.1 11.6 1.0 CD2 A:HIS295 4.2 10.5 1.0 CH3 A:ACT503 4.3 25.8 1.0 CB A:ASP40 4.4 23.9 1.0 OD2 A:ASP39 4.5 7.5 1.0 ND1 A:HIS97 4.6 2.4 1.0 CG A:HIS97 4.7 2.4 1.0 N A:ASP40 4.8 23.9 1.0 CG A:ASP39 4.8 7.5 1.0 CA A:PRO168 4.9 5.6 1.0 CA A:ASP40 4.9 23.9 1.0 OD1 A:ASN65 4.9 3.8 1.0 C2 A:EDO504 5.0 24.4 1.0 N A:TYR169 5.0 8.0 1.0

Zinc binding site 2 out of 4 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:77.6 occ:1.00 OD1 B:ASP40 2.1 24.2 1.0 O B:ACT503 2.2 32.6 1.0 NE2 B:HIS101 2.2 16.0 1.0 NE2 B:HIS97 2.2 10.4 1.0 OXT B:ACT503 2.3 32.6 1.0 C B:ACT503 2.5 32.6 1.0 CD2 B:HIS101 2.7 16.0 1.0 CD2 B:HIS97 3.0 10.4 1.0 CG B:ASP40 3.1 24.2 1.0 O B:HOH601 3.1 23.2 1.0 CE1 B:HIS97 3.4 10.4 1.0 OD2 B:ASP40 3.4 24.2 1.0 CE1 B:HIS101 3.5 16.0 1.0 CH3 B:ACT503 3.9 32.6 1.0 CB B:ASP39 4.0 16.6 1.0 CG B:HIS101 4.0 16.0 1.0 CG B:HIS97 4.2 10.4 1.0 OD2 B:ASP39 4.2 16.6 1.0 ND1 B:HIS101 4.3 16.0 1.0 ND1 B:HIS97 4.3 10.4 1.0 NE2 B:HIS295 4.4 12.9 1.0 CB B:ASP40 4.4 24.2 1.0 N B:ASP40 4.5 24.2 1.0 OD1 B:ASN65 4.6 18.1 1.0 CG B:ASP39 4.6 16.6 1.0 CA B:PRO168 4.6 15.0 1.0 CA B:ASP40 4.7 24.2 1.0 CD2 B:HIS295 4.7 12.9 1.0 CB B:PRO168 4.8 15.0 1.0 C B:ASP39 4.9 16.6 1.0

Zinc binding site 3 out of 4 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 3 of Structure of Vibrio Cholerae Chitin De-N-Acetylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:80.9 occ:1.00 NE2 C:HIS101 2.1 21.7 1.0 OD1 C:ASP40 2.1 38.9 1.0 OXT C:ACT503 2.2 49.2 1.0 O C:ACT503 2.2 49.2 1.0 NE2 C:HIS97 2.3 18.4 1.0 C C:ACT503 2.6 49.2 1.0 CD2 C:HIS101 2.9 21.7 1.0 CD2 C:HIS97 3.1 18.4 1.0 CG C:ASP40 3.1 38.9 1.0 CE1 C:HIS101 3.2 21.7 1.0 O C:HOH601 3.2 15.6 1.0 CE1 C:HIS97 3.3 18.4 1.0 OD2 C:ASP40 3.4 38.9 1.0 CB C:ASP39 3.9 20.6 1.0 CH3 C:ACT503 4.1 49.2 1.0 CG C:HIS101 4.1 21.7 1.0 NE2 C:HIS295 4.1 29.2 1.0 ND1 C:HIS101 4.2 21.7 1.0 OD2 C:ASP39 4.2 20.6 1.0 CG C:HIS97 4.3 18.4 1.0 ND1 C:HIS97 4.4 18.4 1.0 CD2 C:HIS295 4.4 29.2 1.0 CB C:ASP40 4.5 38.9 1.0 CA C:PRO168 4.6 8.7 1.0 CG C:ASP39 4.6 20.6 1.0 N C:ASP40 4.6 38.9 1.0 CB C:PRO168 4.8 8.7 1.0 OD1 C:ASN65 4.8 19.7 1.0 CA C:ASP40 4.8 38.9 1.0 N C:TYR169 4.9 19.1 1.0 C C:ASP39 4.9 20.6 1.0

Zinc binding site 4 out of 4 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 4 of Structure of Vibrio Cholerae Chitin De-N-Acetylase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:88.9 occ:1.00 NE2 D:HIS101 2.1 17.2 1.0 OD1 D:ASP40 2.1 34.0 1.0 NE2 D:HIS97 2.2 13.0 1.0 O D:ACT503 2.3 43.4 1.0 OXT D:ACT503 2.3 43.4 1.0 C D:ACT503 2.7 43.4 1.0 CD2 D:HIS101 3.0 17.2 1.0 CE1 D:HIS101 3.1 17.2 1.0 CD2 D:HIS97 3.1 13.0 1.0 CG D:ASP40 3.2 34.0 1.0 O D:HOH601 3.2 28.9 1.0 CE1 D:HIS97 3.3 13.0 1.0 OD2 D:ASP40 3.5 34.0 1.0 CB D:ASP39 3.9 19.7 1.0 CH3 D:ACT503 4.1 43.4 1.0 ND1 D:HIS101 4.2 17.2 1.0 CG D:HIS101 4.2 17.2 1.0 OD2 D:ASP39 4.2 19.7 1.0 CG D:HIS97 4.3 13.0 1.0 NE2 D:HIS295 4.3 29.1 1.0 ND1 D:HIS97 4.4 13.0 1.0 CA D:PRO168 4.5 13.7 1.0 CB D:ASP40 4.5 34.0 1.0 CG D:ASP39 4.5 19.7 1.0 CD2 D:HIS295 4.5 29.1 1.0 N D:ASP40 4.6 34.0 1.0 CB D:PRO168 4.7 13.7 1.0 CA D:ASP40 4.8 34.0 1.0 N D:TYR169 4.9 13.4 1.0 C D:ASP39 4.9 19.7 1.0 OD1 D:ASN65 5.0 17.2 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