Zinc in PDB 8yh4: Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2

The structure of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2, PDB code: 8yh4 was solved by P.Sirikan, F.Tamo, R.C.Robinson, S.Wipa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.89 / 2.13
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.894, 118.458, 252.574, 90, 90, 90
R / Rfree (%)	15.1 / 18.2

The structure of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 also contains other interesting chemical elements:

Sodium

(Na)

7 atoms

The binding sites of Zinc atom in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 (pdb code 8yh4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2, PDB code: 8yh4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:18.4 occ:1.00 NE2 A:HIS75 2.0 19.1 1.0 O A:HOH661 2.0 18.2 1.0 OD1 A:ASP14 2.2 19.2 1.0 NE2 A:HIS71 2.2 16.0 1.0 O A:HOH731 2.3 15.9 1.0 O3 H:GCS1 2.9 27.6 1.0 CD2 A:HIS75 3.0 17.0 1.0 CE1 A:HIS75 3.1 18.4 1.0 CG A:ASP14 3.1 20.4 1.0 CD2 A:HIS71 3.1 14.4 1.0 OD2 A:ASP14 3.3 21.1 1.0 CE1 A:HIS71 3.3 16.1 1.0 N2 H:GCS1 3.8 35.1 1.0 OD2 A:ASP13 3.9 17.7 1.0 CB A:ASP13 3.9 16.2 1.0 C3 H:GCS1 4.1 32.8 1.0 CG A:HIS75 4.1 19.6 1.0 ND1 A:HIS75 4.1 18.4 1.0 C2 H:GCS1 4.2 33.4 1.0 CG A:HIS71 4.3 15.1 1.0 CG A:ASP13 4.3 20.0 1.0 NE2 A:HIS269 4.3 21.9 1.0 ND1 A:HIS71 4.4 15.5 1.0 CB A:ASP14 4.5 18.3 1.0 CA A:PRO142 4.5 14.3 1.0 CD2 A:HIS269 4.6 20.6 1.0 N A:ASP14 4.6 15.5 1.0 CB A:PRO142 4.8 12.8 1.0 N A:TYR143 4.8 14.8 1.0 CA A:ASP14 4.8 17.4 1.0 C A:ASP13 4.9 17.6 1.0 CA A:ASP13 5.0 16.4 1.0

Zinc binding site 2 out of 4 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:16.3 occ:1.00 O B:HOH743 2.0 14.1 1.0 NE2 B:HIS75 2.1 16.9 1.0 OD1 B:ASP14 2.2 14.6 1.0 O B:HOH751 2.2 13.2 1.0 NE2 B:HIS71 2.3 12.1 1.0 O3 G:GCS1 2.9 21.9 1.0 CD2 B:HIS75 3.0 15.2 1.0 CG B:ASP14 3.0 14.5 1.0 CD2 B:HIS71 3.1 10.9 1.0 CE1 B:HIS75 3.1 15.9 1.0 OD2 B:ASP14 3.3 16.7 1.0 CE1 B:HIS71 3.3 11.3 1.0 N2 G:GCS1 3.8 24.3 1.0 CB B:ASP13 3.9 14.4 1.0 OD2 B:ASP13 4.0 20.4 1.0 C3 G:GCS1 4.1 24.0 1.0 CG B:HIS75 4.1 16.6 1.0 ND1 B:HIS75 4.2 16.0 1.0 C2 G:GCS1 4.2 24.0 1.0 CG B:HIS71 4.3 12.0 1.0 CG B:ASP13 4.4 20.1 1.0 ND1 B:HIS71 4.4 11.1 1.0 NE2 B:HIS269 4.4 18.2 1.0 CB B:ASP14 4.5 13.1 1.0 CA B:PRO142 4.5 13.1 1.0 CD2 B:HIS269 4.6 18.5 1.0 N B:ASP14 4.6 15.8 1.0 CB B:PRO142 4.8 13.6 1.0 N B:TYR143 4.8 15.8 1.0 CA B:ASP14 4.8 15.6 1.0 C B:ASP13 4.9 15.8 1.0 OD1 B:ASN39 4.9 13.6 1.0 CA B:ASP13 5.0 14.9 1.0

Zinc binding site 3 out of 4 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:20.8 occ:1.00 O C:HOH649 2.1 17.1 1.0 NE2 C:HIS75 2.1 24.8 1.0 OD1 C:ASP14 2.2 25.8 1.0 O C:HOH775 2.2 15.8 1.0 NE2 C:HIS71 2.2 15.6 1.0 CD2 C:HIS75 3.0 21.3 1.0 O3 E:GCS1 3.0 23.9 1.0 CG C:ASP14 3.0 22.5 1.0 CD2 C:HIS71 3.1 13.2 1.0 CE1 C:HIS75 3.2 22.8 1.0 OD2 C:ASP14 3.2 22.2 1.0 CE1 C:HIS71 3.3 16.1 1.0 N2 E:GCS1 3.8 25.5 1.0 OD2 C:ASP13 3.8 21.5 1.0 CB C:ASP13 3.9 22.9 1.0 CG C:HIS75 4.2 22.9 1.0 C3 E:GCS1 4.2 24.9 1.0 ND1 C:HIS75 4.2 22.2 1.0 C2 E:GCS1 4.2 26.0 1.0 CG C:HIS71 4.3 15.7 1.0 CG C:ASP13 4.3 22.5 1.0 ND1 C:HIS71 4.4 15.0 1.0 NE2 C:HIS269 4.4 24.4 1.0 CB C:ASP14 4.4 21.3 1.0 CA C:PRO142 4.5 19.0 1.0 CD2 C:HIS269 4.6 23.3 1.0 N C:ASP14 4.6 19.6 1.0 CA C:ASP14 4.8 20.9 1.0 N C:TYR143 4.9 16.4 1.0 CB C:PRO142 4.9 17.9 1.0 OD1 C:ASN39 4.9 20.8 1.0 C C:ASP13 4.9 21.5 1.0 CA C:ASP13 5.0 21.9 1.0

Zinc binding site 4 out of 4 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:23.6 occ:1.00 O D:HOH656 1.9 17.5 1.0 NE2 D:HIS75 2.0 28.4 1.0 OD1 D:ASP14 2.2 29.1 1.0 NE2 D:HIS71 2.3 20.3 1.0 O D:HOH699 2.3 20.6 1.0 O3 F:GCS1 2.9 26.6 1.0 CE1 D:HIS75 3.0 28.2 1.0 CD2 D:HIS75 3.0 26.3 1.0 CD2 D:HIS71 3.1 20.4 1.0 CG D:ASP14 3.1 28.2 1.0 OD2 D:ASP14 3.3 27.9 1.0 CE1 D:HIS71 3.4 21.4 1.0 N2 F:GCS1 3.7 29.6 1.0 OD2 D:ASP13 3.8 26.3 1.0 CB D:ASP13 3.8 23.3 1.0 C3 F:GCS1 4.1 31.2 1.0 ND1 D:HIS75 4.1 27.3 1.0 CG D:HIS75 4.1 27.1 1.0 C2 F:GCS1 4.1 29.3 1.0 CG D:ASP13 4.2 26.1 1.0 CG D:HIS71 4.3 21.3 1.0 NE2 D:HIS269 4.4 28.5 1.0 ND1 D:HIS71 4.4 20.3 1.0 CB D:ASP14 4.5 25.9 1.0 CA D:PRO142 4.5 22.9 1.0 CD2 D:HIS269 4.5 27.3 1.0 N D:ASP14 4.6 20.2 1.0 CB D:PRO142 4.8 20.9 1.0 CA D:ASP14 4.8 24.5 1.0 N D:TYR143 4.9 22.3 1.0 C D:ASP13 4.9 25.1 1.0 CA D:ASP13 4.9 23.9 1.0 OD1 D:ASN39 5.0 24.1 1.0

P.Sirikan, S.Wipa, F.Tamo, R.C.Robinson. Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 To Be Published.