Cadmium in PDB 7vir: Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr

The structure of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr, PDB code: 7vir was solved by C.Lu, X.Peng, B.Maity, N.Ito, S.Abe, T.Ueno, D.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.91 / 1.90
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.213, 180.213, 180.213, 90, 90, 90
R / Rfree (%)	17 / 20.9

The structure of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr also contains other interesting chemical elements:

Gold

(Au)

8 atoms

The binding sites of Cadmium atom in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr (pdb code 7vir). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr, PDB code: 7vir:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


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 Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:22.7 occ:0.25 OE1 A:GLU130 2.3 25.4 1.0 OE2 A:GLU130 2.4 28.6 1.0 CD A:GLU130 2.7 24.0 1.0 AU A:AU213 3.6 29.0 0.7 CG A:GLU130 4.2 22.9 1.0 O A:HOH311 4.2 30.3 1.0 O A:HOH431 4.4 10.0 0.3 SG A:CYS126 4.6 11.0 0.5 CB A:GLU130 4.9 18.7 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


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 Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:30.9 occ:0.15 O A:HOH311 2.3 30.3 1.0 O A:HOH366 2.4 39.6 1.0 OG A:SER131 4.0 24.7 0.5 OD1 A:ASP127 4.1 28.2 1.0 OE1 A:GLU130 4.2 25.4 1.0 CB A:GLU130 4.9 18.7 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


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 Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:29.9 occ:0.20 OE1 A:GLU60 2.5 22.1 1.0 OE2 A:GLU60 2.8 26.7 1.0 CD A:GLU60 3.0 21.6 1.0 OE2 A:GLU56 3.1 41.4 1.0 OE2 A:GLU53 4.0 36.3 1.0 CD A:GLU56 4.2 29.9 1.0 CG A:GLU57 4.5 18.8 1.0 CG A:GLU60 4.5 16.7 1.0 CG A:GLU56 4.6 17.8 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


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 Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd214 b:14.4 occ:0.50 OD2 A:ASP80 2.1 10.3 1.0 OD1 A:ASP80 2.4 10.7 1.0 O A:HOH416 2.5 7.0 1.0 CG A:ASP80 2.6 11.6 1.0 CB A:ASP80 4.1 11.5 1.0 O A:HOH326 4.4 15.8 1.0 O A:HOH355 4.6 21.2 1.0

C.Lu, B.Maity, X.Peng, N.Ito, S.Abe, X.Sheng, T.Ueno, D.Lu. Design of A Gold Clustering Site in An Engineered Apo-Ferritin Cage Commun Chem V. 5 2022.
ISSN: ESSN 2399-3669
DOI: 10.1038/S42004-022-00651-1