Cadmium in PDB 5axs: Crystal Structure of Cdcat-Fn

The structure of Crystal Structure of Cdcat-Fn, PDB code: 5axs was solved by S.Abe, H.Nakajima, M.Kondo, T.Nakane, T.Nakao, T.Ueno, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.81 / 1.67
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.878, 180.878, 180.878, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.8

The binding sites of Cadmium atom in the Crystal Structure of Cdcat-Fn (pdb code 5axs). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Cdcat-Fn, PDB code: 5axs:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Cdcat-Fn


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Cdcat-Fn within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:24.0 occ:0.50 OD1 A:ASP80 2.3 8.4 1.0 OD2 A:ASP80 2.4 26.0 1.0 CG A:ASP80 2.7 14.9 1.0 CB A:ASP80 4.1 14.9 1.0 O A:HOH325 4.4 19.8 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Cdcat-Fn


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Cdcat-Fn within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:34.8 occ:0.33 CD A:CD206 2.2 36.1 0.1 O A:HOH311 2.3 22.9 1.0 OD1 A:ASP127 2.7 20.5 1.0 CG A:ASP127 3.8 19.0 1.0 OG A:SER131 4.1 23.2 1.0 OD2 A:ASP127 4.2 17.6 1.0 OE1 A:GLU130 4.3 20.2 1.0 CD A:CD205 4.7 44.5 0.3

Cadmium binding site 3 out of 5 in the Crystal Structure of Cdcat-Fn


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Cdcat-Fn within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:43.7 occ:0.33 O6 A:4LF201 2.2 23.9 1.0 O5 A:4LF201 2.2 24.0 1.0 C15 A:4LF201 3.0 24.2 1.0 C16 A:4LF201 3.0 26.5 1.0 O A:HOH305 3.9 25.5 1.0 O A:HOH411 4.0 27.4 1.0 C14 A:4LF201 4.3 22.3 1.0 C11 A:4LF201 4.3 26.8 1.0 N3 A:4LF201 4.6 33.9 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of Cdcat-Fn


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Cdcat-Fn within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:44.5 occ:0.33 O A:HOH316 1.6 20.9 1.0 OE1 A:GLU130 2.5 20.2 1.0 CD A:GLU130 3.3 18.1 1.0 OE2 A:GLU130 3.3 19.6 1.0 OD1 A:ASP127 4.2 20.5 1.0 O A:HOH305 4.4 25.5 1.0 CD A:CD203 4.7 34.8 0.3 CG A:GLU130 4.7 13.0 1.0 CG A:ASP127 5.0 19.0 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Cdcat-Fn


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Cdcat-Fn within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:36.1 occ:0.10 O A:HOH311 2.0 22.9 1.0 CD A:CD203 2.2 34.8 0.3 OG A:SER131 3.5 23.2 1.0 OD1 A:ASP127 4.0 20.5 1.0 OD2 A:ASP127 4.6 17.6 1.0 CG A:ASP127 4.7 19.0 1.0 CB A:SER131 4.7 15.7 1.0

H.Nakajima, M.Kondo, T.Nakane, S.Abe, T.Nakao, Y.Watanabe, T.Ueno. Construction of An Enterobactin Analogue with Symmetrically Arranged Monomer Subunits of Ferritin Chem.Commun.(Camb.) V. 51 16609 2015.
ISSN: ESSN 1364-548X
PubMed: 26404005
DOI: 10.1039/C5CC06904A