Cadmium in PDB 6jef: Crystal Structure of Apo-R168C/L169C-Fr

The structure of Crystal Structure of Apo-R168C/L169C-Fr, PDB code: 6jef 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)	27.71 / 1.58
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.606, 181.606, 181.606, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 18.2

The structure of Crystal Structure of Apo-R168C/L169C-Fr also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Crystal Structure of Apo-R168C/L169C-Fr (pdb code 6jef). 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-R168C/L169C-Fr, PDB code: 6jef:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Apo-R168C/L169C-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-R168C/L169C-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:17.3 occ:0.50 OD2 A:ASP80 1.8 14.2 1.0 OD1 A:ASP80 2.4 12.1 1.0 CL A:CL207 2.5 27.2 1.0 CG A:ASP80 2.5 15.3 1.0 CB A:ASP80 4.1 14.4 1.0 O A:HOH315 4.3 18.5 1.0 O A:HOH399 4.6 19.9 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Apo-R168C/L169C-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-R168C/L169C-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:37.3 occ:0.10 O A:HOH339 2.0 37.4 1.0 O A:HOH332 2.1 38.4 0.3 OE1 A:GLU130 2.4 24.6 1.0 CD A:GLU130 3.4 22.0 1.0 OE2 A:GLU130 3.5 20.8 1.0 OD1 A:ASP127 4.3 25.9 1.0 CD A:CD204 4.4 37.6 0.1 CG A:GLU130 4.7 16.2 1.0 CB A:ASP127 4.9 15.0 1.0 CG A:ASP127 5.0 20.0 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of Apo-R168C/L169C-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-R168C/L169C-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:37.6 occ:0.10 O A:HOH330 2.3 32.9 1.0 O A:HOH332 2.4 38.4 0.3 CD A:CD206 2.5 40.1 0.1 OD1 A:ASP127 2.7 25.9 1.0 CG A:ASP127 3.8 20.0 1.0 OG A:SER131 4.0 24.9 1.0 OD2 A:ASP127 4.3 23.8 1.0 OE1 A:GLU130 4.4 24.6 1.0 CD A:CD203 4.4 37.3 0.1

Cadmium binding site 4 out of 5 in the Crystal Structure of Apo-R168C/L169C-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-R168C/L169C-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:31.7 occ:0.40 CB A:CYS168 2.1 33.4 1.0 CA A:CYS168 3.0 37.4 1.0 C A:CYS168 3.2 39.4 1.0 N A:CYS169 3.6 36.5 1.0 O A:CYS168 3.7 43.2 1.0 N A:CYS168 4.3 31.5 1.0 CA A:CYS169 4.3 34.0 1.0 CB A:CYS169 4.6 41.3 1.0 O A:LEU165 4.7 25.6 1.0 CD2 A:LEU165 4.8 33.0 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Apo-R168C/L169C-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-R168C/L169C-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:40.1 occ:0.10 O A:HOH330 2.3 32.9 1.0 CD A:CD204 2.5 37.6 0.1 OG A:SER131 3.8 24.9 1.0 OD1 A:ASP127 4.3 25.9 1.0 CB A:SER131 4.8 18.7 1.0 O A:HOH332 4.8 38.4 0.3

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