Cadmium in PDB 7w7j: Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (25 Equiv)

The structure of Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (25 Equiv), PDB code: 7w7j was solved by M.Taher, B.Maity, T.Nakane, S.Abe, S.Mazumdar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.09 / 1.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.995, 181.995, 181.995, 90, 90, 90
R / Rfree (%)	18.3 / 21

The structure of Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (25 Equiv) also contains other interesting chemical elements:

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

The binding sites of Cadmium atom in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (25 Equiv) (pdb code 7w7j). 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 Ircp* Immobilized Apo-R52H-Rhlfr (25 Equiv), PDB code: 7w7j:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (25 Equiv)


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 (25 Equiv) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:16.8 occ:0.25 CD A:CD207 1.2 13.2 0.2 CL A:CL208 2.1 65.8 1.0 OD1 A:ASP80 2.7 20.4 1.0 OD2 A:ASP80 2.8 27.5 1.0 CG A:ASP80 3.1 22.3 1.0 O A:HOH375 4.5 23.8 1.0 CB A:ASP80 4.7 18.8 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (25 Equiv)


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 (25 Equiv) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:32.8 occ:0.15 O A:HOH302 2.3 31.6 1.0 O A:HOH343 2.4 43.6 1.0 OD1 A:ASP127 3.6 21.1 1.0 O A:HOH323 4.0 40.5 1.0 CD A:CD205 4.1 25.8 0.1 OE1 A:GLU130 4.2 27.7 1.0 OG A:SER131 4.3 29.8 1.0 CG A:ASP127 4.8 20.3 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (25 Equiv)


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 (25 Equiv) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:25.8 occ:0.10 CD A:CD206 1.6 15.7 0.2 OE1 A:GLU130 2.3 27.7 1.0 CD A:GLU130 3.3 24.2 1.0 OE2 A:GLU130 3.5 22.2 1.0 O A:HOH302 3.7 31.6 1.0 CD A:CD204 4.1 32.8 0.1 CG A:GLU130 4.6 20.4 1.0 CB A:GLU130 5.0 19.4 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (25 Equiv)


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 (25 Equiv) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:15.7 occ:0.20 CD A:CD205 1.6 25.8 0.1 OE1 A:GLU130 2.6 27.7 1.0 OE2 A:GLU130 2.9 22.2 1.0 CD A:GLU130 3.0 24.2 1.0 O A:HOH443 4.0 12.8 1.0 O A:HOH302 4.1 31.6 1.0 N A:ASP127 4.3 13.1 1.0 CA A:ASP127 4.4 14.2 1.0 CG A:GLU130 4.5 20.4 1.0 C A:CYS126 4.6 13.4 1.0 CB A:CYS126 4.6 15.0 1.0 O A:CYS126 4.8 13.1 1.0 CB A:ASP127 4.8 16.6 1.0 O A:HOH509 4.8 32.5 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (25 Equiv)


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 (25 Equiv) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:13.2 occ:0.25 CD A:CD203 1.2 16.8 0.2 OD2 A:ASP80 1.9 27.5 1.0 OD1 A:ASP80 2.5 20.4 1.0 CG A:ASP80 2.5 22.3 1.0 CL A:CL208 3.1 65.8 1.0 CB A:ASP80 3.9 18.8 1.0 O A:HOH375 4.5 23.8 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