Cadmium in PDB 6jee: Crystal Structure of Apo-L161C/L165C-Fr

The structure of Crystal Structure of Apo-L161C/L165C-Fr, PDB code: 6jee was solved by S.Abe, N.Ito, B.Maity, C.Lu, D.Lu, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.54 / 1.30
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	182.264, 182.264, 182.264, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 17

The structure of Crystal Structure of Apo-L161C/L165C-Fr also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Crystal Structure of Apo-L161C/L165C-Fr (pdb code 6jee). 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 Apo-L161C/L165C-Fr, PDB code: 6jee:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Apo-L161C/L165C-Fr


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 Apo-L161C/L165C-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:52.7 occ:0.20 O A:HOH334 1.9 21.2 0.3 O A:HOH352 2.3 27.6 1.0 OE1 A:GLU130 2.4 18.1 1.0 CD A:GLU130 3.4 14.1 1.0 OE2 A:GLU130 3.7 13.6 1.0 O A:HOH307 3.8 30.4 0.3 OD1 A:ASP127 3.9 18.5 1.0 O A:HOH372 4.4 27.5 1.0 CG A:ASP127 4.7 15.6 1.0 CG A:GLU130 4.8 11.6 1.0 CB A:ASP127 4.9 11.7 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Apo-L161C/L165C-Fr


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 Apo-L161C/L165C-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:25.8 occ:0.10 O A:HOH305 2.2 31.1 1.0 O A:HOH307 2.5 30.4 0.3 OG A:SER131 3.8 16.9 1.0 OD1 A:ASP127 4.1 18.5 1.0 O A:HOH334 4.4 21.2 0.3 OD2 A:ASP127 4.7 18.1 1.0 CG A:ASP127 4.8 15.6 1.0 CB A:SER131 4.9 12.6 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of Apo-L161C/L165C-Fr


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 Apo-L161C/L165C-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:7.4 occ:0.50 CL A:CL210 2.3 14.0 1.0 OD1 A:ASP80 2.4 7.8 1.0 OD2 A:ASP80 2.5 9.1 1.0 CG A:ASP80 2.8 7.2 1.0 CB A:ASP80 4.3 7.6 1.0 O A:HOH422 4.5 12.9 1.0 O A:HOH337 4.8 14.3 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of Apo-L161C/L165C-Fr


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 Apo-L161C/L165C-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:33.0 occ:0.60 SG A:CYS161 2.4 40.4 1.0 O A:HOH478 2.4 42.3 1.0 SG A:CYS165 2.4 25.0 1.0 O A:CYS161 2.7 25.6 1.0 C A:CYS161 3.3 27.8 1.0 CD A:CD205 3.4 24.7 0.2 CB A:CYS165 3.4 15.8 1.0 CB A:CYS161 3.7 29.7 1.0 CA A:CYS161 3.7 28.6 1.0 N A:GLY162 4.1 22.3 1.0 N A:CYS165 4.5 12.1 1.0 CA A:CYS165 4.5 13.6 1.0 CA A:GLY162 4.6 23.3 1.0 CD2 A:LEU154 4.9 22.2 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Apo-L161C/L165C-Fr


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 Apo-L161C/L165C-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:24.7 occ:0.20 O A:HOH508 2.3 33.6 0.2 SG A:CYS165 2.5 25.0 1.0 CD A:CD204 3.4 33.0 0.6 CB A:CYS165 4.3 15.8 1.0 O A:HOH478 4.8 42.3 1.0

S.Abe, N.Ito, B.Maity, C.Lu, D.Lu, T.Ueno. Coordination Design of Cadmium Ions at the 4-Fold Axis Channel of the Apo-Ferritin Cage. Dalton Trans V. 48 9759 2019.
ISSN: ESSN 1477-9234
PubMed: 30993287
DOI: 10.1039/C9DT00609E