Cadmium in PDB 7eml: Structure of Ircp* Immobilized Apo-D38H-Rhlfr

The structure of Structure of Ircp* Immobilized Apo-D38H-Rhlfr, PDB code: 7eml 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)	41.74 / 1.25
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.937, 181.937, 181.937, 90, 90, 90
R / Rfree (%)	17.1 / 18.3

The structure of Structure of Ircp* Immobilized Apo-D38H-Rhlfr also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Iridium	(Ir)	5 atoms

The binding sites of Cadmium atom in the Structure of Ircp* Immobilized Apo-D38H-Rhlfr (pdb code 7eml). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of Ircp* Immobilized Apo-D38H-Rhlfr, PDB code: 7eml:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Structure of Ircp* Immobilized Apo-D38H-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Ircp* Immobilized Apo-D38H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:11.1 occ:0.40 CD A:CD210 1.2 10.8 0.1 OD1 A:ASP80 2.3 12.9 1.0 OD2 A:ASP80 2.4 15.8 1.0 CL A:CL211 2.5 23.4 1.0 CG A:ASP80 2.7 14.4 1.0 CB A:ASP80 4.2 14.0 1.0 O A:HOH414 4.4 19.9 1.0 O A:HOH349 4.6 20.2 1.0

Cadmium binding site 2 out of 5 in the Structure of Ircp* Immobilized Apo-D38H-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Ircp* Immobilized Apo-D38H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:24.2 occ:0.10 O A:HOH307 2.3 34.4 1.0 O A:HOH369 2.3 36.2 1.0 OD1 A:ASP127 3.7 24.0 1.0 CD A:CD208 4.0 22.6 0.1 OE1 A:GLU130 4.1 28.4 1.0 OG A:SER131 4.2 26.3 1.0 CG A:ASP127 4.8 20.2 1.0

Cadmium binding site 3 out of 5 in the Structure of Ircp* Immobilized Apo-D38H-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Ircp* Immobilized Apo-D38H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:22.6 occ:0.10 CD A:CD209 1.7 14.9 0.1 OE1 A:GLU130 2.3 28.4 1.0 CD A:GLU130 3.3 24.8 1.0 O A:HOH307 3.5 34.4 1.0 OE2 A:GLU130 3.6 21.4 1.0 CD A:CD207 4.0 24.2 0.1 O A:HOH314 4.3 29.6 1.0 CG A:GLU130 4.7 18.6 1.0

Cadmium binding site 4 out of 5 in the Structure of Ircp* Immobilized Apo-D38H-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Ircp* Immobilized Apo-D38H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd209 b:14.9 occ:0.15 CD A:CD208 1.7 22.6 0.1 OE1 A:GLU130 2.6 28.4 1.0 O A:HOH314 2.8 29.6 1.0 OE2 A:GLU130 2.9 21.4 1.0 CD A:GLU130 3.0 24.8 1.0 CG A:GLU130 4.3 18.6 1.0 IR A:IR212 4.4 34.9 0.1 O A:HOH500 4.7 30.4 1.0 O A:HOH307 4.8 34.4 1.0 CB A:GLU130 5.0 17.6 1.0

Cadmium binding site 5 out of 5 in the Structure of Ircp* Immobilized Apo-D38H-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Ircp* Immobilized Apo-D38H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd210 b:10.8 occ:0.10 CD A:CD206 1.2 11.1 0.4 OD2 A:ASP80 1.6 15.8 1.0 CG A:ASP80 2.1 14.4 1.0 OD1 A:ASP80 2.2 12.9 1.0 CL A:CL211 3.4 23.4 1.0 CB A:ASP80 3.5 14.0 1.0 O A:HOH349 3.6 20.2 1.0 O A:HOH414 4.4 19.9 1.0 CA A:ASP80 4.7 12.5 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