Calcium in PDB 8yfp: Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod)

The structure of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod), PDB code: 8yfp 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)	19.93 / 2.45
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	209.061, 209.061, 209.061, 90, 90, 90
R / Rfree (%)	19.5 / 21.9

The structure of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Magnesium	(Mg)	2 atoms

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

Calcium binding site 1 out of 3 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:58.1 occ:1.00 O A:HOH703 2.5 47.9 1.0 O A:LYS196 2.5 34.2 1.0 O B:HOH646 2.6 53.9 1.0 O A:HOH706 2.7 41.3 1.0 O A:HOH679 2.8 36.3 1.0 C A:LYS196 3.7 31.8 1.0 OE2 B:GLU136 4.4 59.9 1.0 O A:GLU136 4.4 33.5 1.0 CA A:GLY197 4.6 29.3 1.0 N A:GLY197 4.6 29.7 1.0 CA A:LYS196 4.6 34.0 1.0 O B:HOH678 4.6 55.6 1.0 CB A:LYS196 4.6 33.9 1.0 OE1 B:GLU136 4.8 60.6 1.0

Calcium binding site 2 out of 3 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:116.0 occ:1.00 O B:HOH716 2.4 96.5 1.0 OD1 B:ASP82 2.8 93.0 1.0 O B:HOH723 3.0 83.8 1.0 OE2 B:GLU83 3.0 93.5 1.0 CG B:ASP82 3.9 86.2 1.0 CD B:GLU83 4.2 94.7 1.0 OD2 B:ASP82 4.7 90.1 1.0 CB B:ASP82 4.8 72.8 1.0 OE1 B:GLU83 4.9 99.9 1.0

Calcium binding site 3 out of 3 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:37.8 occ:1.00 O B:GLY197 2.2 31.9 1.0 O B:GLY329 2.2 34.7 1.0 O B:HOH680 2.4 33.4 1.0 O B:HOH706 2.4 38.0 1.0 OE2 B:GLU137 2.4 44.5 1.0 O B:HOH666 2.4 32.9 1.0 C B:GLY329 3.3 33.2 1.0 C B:GLY197 3.3 32.3 1.0 CD B:GLU137 3.6 45.6 1.0 CA B:GLY329 3.9 33.0 1.0 CA B:GLY197 3.9 35.2 1.0 N B:THR330 4.3 33.6 1.0 OE1 B:GLU137 4.3 54.4 1.0 N B:TYR198 4.4 31.6 1.0 CA B:THR330 4.5 35.0 1.0 O B:GLU137 4.6 33.2 1.0 CB B:GLU137 4.6 34.5 1.0 OD2 B:ASP357 4.7 36.9 1.0 CG B:GLU137 4.7 38.6 1.0 CA B:TYR198 4.7 33.3 1.0 CA B:GLU137 4.7 34.2 1.0 C B:TYR198 4.9 32.5 1.0 OD1 B:ASP357 5.0 41.7 1.0

P.Sirikan, S.Wipa, F.Tamo, R.C.Robinson. Structural and Functional of Chito Oligosaccharide Deacetylase of Vibrio Cambellii To Be Published.