Zinc in PDB 3wx7: Crystal Structure of Cod

The structure of Crystal Structure of Cod, PDB code: 3wx7 was solved by S.-Y.Park, K.Sugiyama, T.Hirano, T.Nishio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.81 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.819, 104.106, 140.378, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 19.8

The structure of Crystal Structure of Cod also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Cod (pdb code 3wx7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Cod, PDB code: 3wx7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Cod


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Cod within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:12.1 occ:1.00 NE2 A:HIS97 2.2 12.9 1.0 OD1 A:ASP36 2.2 13.6 1.0 NE2 A:HIS93 2.2 9.9 1.0 OXT A:ACT903 2.3 20.9 1.0 O A:HOH1131 2.3 20.3 1.0 O A:ACT903 2.4 14.1 1.0 C A:ACT903 2.7 21.8 1.0 CD2 A:HIS97 3.0 12.0 1.0 CG A:ASP36 3.0 14.7 1.0 CD2 A:HIS93 3.1 9.9 1.0 OD2 A:ASP36 3.2 16.1 1.0 CE1 A:HIS97 3.2 12.6 1.0 CE1 A:HIS93 3.2 10.2 1.0 CB A:ASP35 3.9 11.1 1.0 OD2 A:ASP35 4.0 13.1 1.0 CH3 A:ACT903 4.1 20.1 1.0 CG A:HIS97 4.2 11.6 1.0 NE2 A:HIS291 4.2 17.4 1.0 ND1 A:HIS97 4.3 13.3 1.0 CG A:HIS93 4.3 10.0 1.0 ND1 A:HIS93 4.3 9.4 1.0 O A:HOH1381 4.3 28.4 1.0 CG A:ASP35 4.4 10.6 1.0 CB A:ASP36 4.5 12.4 1.0 CD2 A:HIS291 4.6 15.3 1.0 CA A:PRO164 4.6 11.3 1.0 N A:ASP36 4.7 11.8 1.0 OD1 A:ASN61 4.8 11.3 1.0 CA A:ASP36 4.9 11.9 1.0 C A:ASP35 4.9 11.8 1.0 N A:TYR165 5.0 12.0 1.0 CB A:PRO164 5.0 11.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Cod


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Cod within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:11.2 occ:1.00 NE2 B:HIS97 2.1 12.9 1.0 NE2 B:HIS93 2.2 10.4 1.0 OD1 B:ASP36 2.2 12.7 1.0 OXT B:ACT903 2.2 19.2 1.0 O B:HOH1189 2.4 22.5 1.0 O B:ACT903 2.4 12.9 1.0 C B:ACT903 2.7 18.6 1.0 CD2 B:HIS97 3.0 12.8 1.0 CG B:ASP36 3.0 12.5 1.0 CD2 B:HIS93 3.1 10.6 1.0 OD2 B:ASP36 3.2 13.2 1.0 CE1 B:HIS97 3.2 11.6 1.0 CE1 B:HIS93 3.2 8.8 1.0 CB B:ASP35 3.9 11.1 1.0 OD2 B:ASP35 4.0 14.1 1.0 CH3 B:ACT903 4.1 19.7 1.0 CG B:HIS97 4.2 12.4 1.0 NE2 B:HIS291 4.2 14.3 1.0 ND1 B:HIS97 4.2 12.5 1.0 CG B:HIS93 4.3 9.5 1.0 ND1 B:HIS93 4.3 9.7 1.0 CG B:ASP35 4.4 10.8 1.0 CB B:ASP36 4.4 10.6 1.0 CD2 B:HIS291 4.6 11.8 1.0 CA B:PRO164 4.6 9.4 1.0 N B:ASP36 4.7 10.3 1.0 OD1 B:ASN61 4.8 11.6 1.0 CA B:ASP36 4.9 10.2 1.0 C B:ASP35 4.9 10.4 1.0 CB B:PRO164 5.0 10.3 1.0

T.Hirano, K.Sugiyama, Y.Sakaki, W.Hakamata, S.-Y.Park, T.Nishio. Structural and Functional Analysis of Chitin Oligosaccharide Deacetylase From Vivrio Parahaemolyticus To Be Published.