Calcium 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:

Zinc

(Zn)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Cod within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:12.6 occ:1.00 O A:GLY351 2.1 9.1 1.0 O A:GLY219 2.1 8.1 1.0 O A:HOH1034 2.1 11.7 1.0 O A:HOH1014 2.1 9.9 1.0 O A:HOH1027 2.1 11.1 1.0 O A:HOH1012 2.1 9.5 1.0 C A:GLY219 3.2 7.8 1.0 C A:GLY351 3.2 7.5 1.0 CA A:GLY219 3.7 8.1 1.0 CA A:GLY351 3.9 9.8 1.0 O A:HOH1163 4.1 20.4 1.0 O A:HOH1019 4.2 10.4 1.0 O A:HOH1176 4.2 21.9 1.0 N A:THR352 4.2 7.5 1.0 O A:HOH1048 4.2 13.5 1.0 OD2 A:ASP379 4.2 12.4 1.0 N A:TYR220 4.3 6.6 1.0 OD1 A:ASP379 4.3 9.6 1.0 CA A:THR352 4.4 6.9 1.0 O A:HOH1232 4.5 23.2 1.0 CA A:TYR220 4.6 7.1 1.0 C A:TYR220 4.6 7.6 1.0 CG A:ASP379 4.7 9.5 1.0 O A:GLU159 4.8 7.6 1.0 N A:GLN221 4.8 6.5 1.0 CG A:GLU159 4.9 11.6 1.0 OG1 A:THR352 5.0 12.1 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Cod within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:13.2 occ:1.00 O B:GLY351 2.1 8.9 1.0 O B:GLY219 2.1 8.9 1.0 O B:HOH1040 2.1 12.3 1.0 O B:HOH1049 2.1 12.9 1.0 O B:HOH1031 2.1 11.8 1.0 O B:HOH1016 2.2 10.3 1.0 C B:GLY219 3.2 8.3 1.0 C B:GLY351 3.2 8.8 1.0 CA B:GLY219 3.7 9.2 1.0 CA B:GLY351 3.9 10.8 1.0 O B:HOH1173 4.0 20.4 1.0 O B:HOH1265 4.2 23.3 1.0 N B:THR352 4.2 8.2 1.0 O B:HOH1019 4.2 11.1 1.0 O B:HOH1066 4.2 14.5 1.0 OD2 B:ASP379 4.3 12.3 1.0 N B:TYR220 4.3 8.0 1.0 O B:HOH1276 4.4 24.2 1.0 OD1 B:ASP379 4.4 10.8 1.0 CA B:THR352 4.4 8.1 1.0 CA B:TYR220 4.6 9.3 1.0 C B:TYR220 4.6 8.4 1.0 CG B:ASP379 4.7 9.5 1.0 N B:GLN221 4.7 7.4 1.0 O B:GLU159 4.8 9.6 1.0 CG B:GLU159 4.9 13.3 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.