Cadmium in PDB 8c6z: Necrotic Enteritis Associated Clostridium P. Chitinase F8UNI4 in Complex with Inhibitor Bisdionin C

The structure of Necrotic Enteritis Associated Clostridium P. Chitinase F8UNI4 in Complex with Inhibitor Bisdionin C, PDB code: 8c6z was solved by Y.Bloch, S.N.Savvides, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.94 / 1.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.401, 67.401, 355.823, 90, 90, 90
R / Rfree (%)	19.7 / 22.3

The structure of Necrotic Enteritis Associated Clostridium P. Chitinase F8UNI4 in Complex with Inhibitor Bisdionin C also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Cadmium atom in the Necrotic Enteritis Associated Clostridium P. Chitinase F8UNI4 in Complex with Inhibitor Bisdionin C (pdb code 8c6z). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Necrotic Enteritis Associated Clostridium P. Chitinase F8UNI4 in Complex with Inhibitor Bisdionin C, PDB code: 8c6z:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Necrotic Enteritis Associated Clostridium P. Chitinase F8UNI4 in Complex with Inhibitor Bisdionin C


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Necrotic Enteritis Associated Clostridium P. Chitinase F8UNI4 in Complex with Inhibitor Bisdionin C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd702 b:35.5 occ:1.00 N9 A:DW0704 2.4 36.5 1.0 OD1 A:ASP34 2.4 24.4 1.0 O A:HOH1157 2.5 23.0 1.0 SG A:CYS73 2.6 36.3 1.0 OD2 A:ASP34 2.6 29.7 1.0 CG A:ASP34 2.8 27.9 1.0 C8 A:DW0704 3.3 36.9 1.0 CAC A:DW0704 3.3 36.6 1.0 C4 A:DW0704 3.4 36.6 1.0 CB A:CYS73 3.5 31.4 1.0 N3 A:DW0704 3.8 36.6 1.0 CB A:ASP74 4.2 34.2 1.0 CB A:ASP34 4.3 23.0 1.0 CE3 A:TRP35 4.5 30.5 1.0 N A:TRP35 4.5 27.2 1.0 CB A:TRP35 4.5 26.0 1.0 O A:HOH1176 4.5 42.1 1.0 N7 A:DW0704 4.5 36.6 1.0 C A:CYS73 4.5 31.6 1.0 N A:ASP74 4.5 29.6 1.0 C5 A:DW0704 4.6 36.6 1.0 CA A:CYS73 4.7 31.9 1.0 C A:ASP34 4.8 28.2 1.0 CA A:TRP35 4.9 28.5 1.0 O A:HOH879 5.0 30.8 1.0 O A:CYS73 5.0 30.9 1.0 CA A:ASP74 5.0 29.6 1.0

Cadmium binding site 2 out of 2 in the Necrotic Enteritis Associated Clostridium P. Chitinase F8UNI4 in Complex with Inhibitor Bisdionin C


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Necrotic Enteritis Associated Clostridium P. Chitinase F8UNI4 in Complex with Inhibitor Bisdionin C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd703 b:36.2 occ:1.00 OE2 A:GLU177 2.3 36.6 1.0 OD1 A:ASP63 2.4 29.4 1.0 OD2 A:ASP125 2.4 34.9 1.0 O A:HOH840 2.5 36.0 1.0 O A:PHE64 2.5 33.2 1.0 O A:HOH1111 2.7 39.1 1.0 OE1 A:GLU177 2.9 35.4 1.0 CD A:GLU177 2.9 40.3 1.0 CG A:ASP63 3.3 35.2 1.0 OD2 A:ASP63 3.5 36.2 1.0 CG A:ASP125 3.5 42.0 1.0 C A:PHE64 3.6 37.5 1.0 N A:PHE64 3.9 35.8 1.0 CB A:ASP125 3.9 38.7 1.0 O A:HOH810 4.1 38.8 1.0 O A:LYS122 4.1 31.4 1.0 O A:HOH1160 4.2 52.6 1.0 CA A:ASN65 4.4 35.0 1.0 CG A:GLU177 4.4 33.3 1.0 N A:ASN65 4.4 38.2 1.0 CA A:PHE64 4.4 32.9 1.0 N A:ASP125 4.4 36.2 1.0 OD1 A:ASP125 4.6 34.8 1.0 CB A:ASP63 4.7 30.6 1.0 C A:LYS122 4.7 36.5 1.0 CD A:LYS122 4.8 35.9 1.0 CA A:LYS122 4.8 35.1 1.0 CA A:ASP125 4.9 40.1 1.0 CB A:LYS122 4.9 33.7 1.0 C A:ASP63 5.0 31.2 1.0 CD2 A:PHE64 5.0 33.2 1.0

Y.Bloch, E.Dierick, E.Goossens, S.N.Savvides. Contribution and Structural Characterization of Chitinases to Clostridium Perfringens Pathogenesis in Broilers To Be Published.