Cadmium in PDB 7emm: Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr

The structure of Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr, PDB code: 7emm was solved by M.Taher, B.Maity, T.Nakane, S.Abe, T.Ueno, S.Mazumdar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.77 / 1.25
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	182.064, 182.064, 182.064, 90, 90, 90
R / Rfree (%)	17.5 / 18.6

The structure of Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Iridium	(Ir)	6 atoms

The binding sites of Cadmium atom in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (pdb code 7emm). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr, PDB code: 7emm:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:10.9 occ:0.35 CD A:CD205 1.3 10.8 0.1 OD2 A:ASP80 2.4 16.4 1.0 OD1 A:ASP80 2.4 13.8 1.0 CL A:CL216 2.5 25.4 1.0 CG A:ASP80 2.8 16.0 1.0 CB A:ASP80 4.3 14.1 1.0 O A:HOH413 4.4 19.4 1.0 O A:HOH326 4.5 23.0 1.0

Cadmium binding site 2 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:10.8 occ:0.15 CD A:CD204 1.3 10.9 0.3 OD2 A:ASP80 1.6 16.4 1.0 CG A:ASP80 2.2 16.0 1.0 OD1 A:ASP80 2.3 13.8 1.0 CL A:CL216 3.4 25.4 1.0 O A:HOH326 3.5 23.0 1.0 CB A:ASP80 3.5 14.1 1.0 O A:HOH413 4.4 19.4 1.0 CA A:ASP80 4.7 12.3 1.0

Cadmium binding site 3 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:44.9 occ:0.10 O A:HOH306 2.2 31.7 1.0 O A:HOH341 2.5 33.4 1.0 CD A:CD207 3.7 24.4 0.1 OD1 A:ASP127 3.7 22.0 1.0 OE1 A:GLU130 3.9 26.4 1.0 O A:HOH344 4.3 43.2 1.0 OG A:SER131 4.4 25.0 1.0 CG A:ASP127 4.8 19.3 1.0 CD A:CD208 4.9 17.8 0.2 CB A:GLU130 4.9 15.1 1.0

Cadmium binding site 4 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:24.4 occ:0.10 CD A:CD208 1.7 17.8 0.2 OE1 A:GLU130 2.3 26.4 1.0 CD A:GLU130 3.3 23.1 1.0 O A:HOH306 3.5 31.7 1.0 OE2 A:GLU130 3.6 20.0 1.0 CD A:CD206 3.7 44.9 0.1 O A:HOH316 4.3 31.8 1.0 CG A:GLU130 4.6 16.9 1.0 CB A:GLU130 5.0 15.1 1.0

Cadmium binding site 5 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr


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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:17.8 occ:0.20 CD A:CD207 1.7 24.4 0.1 OE1 A:GLU130 2.4 26.4 1.0 OE2 A:GLU130 2.9 20.0 1.0 CD A:GLU130 3.0 23.1 1.0 O A:HOH306 3.9 31.7 1.0 IR A:IR210 4.0 26.8 0.1 N A:ASP127 4.3 11.3 1.0 CA A:ASP127 4.3 12.5 1.0 O A:HOH316 4.3 31.8 1.0 CG A:GLU130 4.5 16.9 1.0 C A:CYS126 4.6 11.3 1.0 CB A:ASP127 4.6 16.7 1.0 CB A:CYS126 4.6 12.1 1.0 O A:CYS126 4.8 12.5 1.0 CD A:CD206 4.9 44.9 0.1

Cadmium binding site 6 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd209 b:22.2 occ:0.15 O A:HOH372 1.9 41.1 1.0 NE2 A:HIS132 2.2 24.0 1.0 CE1 A:HIS132 2.8 23.4 1.0 CD2 A:HIS132 3.4 21.1 1.0 O A:HOH350 4.0 44.3 1.0 ND1 A:HIS132 4.1 21.9 1.0 CG A:HIS132 4.4 18.6 1.0 NH1 A:ARG64 4.5 34.7 1.0

M.Taher, B.Maity, T.Nakane, S.Abe, T.Ueno, S.Mazumdar. Controlled Uptake of An Iridium Complex Inside Engineered Apo-Ferritin Nanocages: Study of Structure and Catalysis. Angew.Chem.Int.Ed.Engl. V. 61 16623 2022.
ISSN: ESSN 1521-3773
PubMed: 35005820
DOI: 10.1002/ANIE.202116623