Iridium 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:

Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	1 atom

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

Iridium 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 Iridium with other atoms in the Ir binding site number 1 of Structure of Ircp* Immobilized Apo-D38H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir201 b:13.8 occ:0.30 IR1 A:RIR201 0.0 13.8 0.3 IR A:IR213 1.3 23.0 0.2 ND1 A:HIS38 2.0 28.7 1.0 C17 A:RIR201 2.1 13.4 0.3 C19 A:RIR201 2.1 14.4 0.3 C20 A:RIR201 2.1 14.1 0.3 C21 A:RIR201 2.1 12.9 0.3 C18 A:RIR201 2.2 13.6 0.3 SG A:CYS48 2.2 16.0 1.0 CE1 A:HIS38 2.9 29.0 1.0 CG A:HIS38 3.2 23.2 1.0 C23 A:RIR201 3.2 15.2 0.3 C26 A:RIR201 3.2 13.8 0.3 C25 A:RIR201 3.3 14.8 0.3 C22 A:RIR201 3.3 14.0 0.3 C24 A:RIR201 3.4 15.4 0.3 CB A:CYS48 3.5 12.2 1.0 CB A:HIS38 3.7 18.6 1.0 ND1 A:HIS49 4.1 23.2 0.7 NE2 A:HIS38 4.1 29.0 1.0 CE1 A:HIS49 4.2 22.6 0.7 CD2 A:HIS38 4.2 25.9 1.0 CA A:CYS48 4.8 11.5 1.0 C A:CYS48 4.9 10.8 1.0 O A:GLY34 5.0 12.5 1.0

Iridium 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 Iridium with other atoms in the Ir binding site number 2 of Structure of Ircp* Immobilized Apo-D38H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir212 b:34.9 occ:0.15 O A:HOH462 1.8 39.5 1.0 NE2 A:HIS114 2.6 15.8 1.0 CE1 A:HIS114 3.0 11.4 1.0 OE2 A:GLU130 3.2 21.4 1.0 O A:HOH500 3.3 30.4 1.0 CB A:CYS126 3.6 13.7 1.0 CD2 A:HIS114 3.8 12.5 1.0 OG A:SER118 3.8 17.7 0.5 O A:HOH314 3.9 29.6 1.0 SG A:CYS126 3.9 14.9 1.0 ND1 A:HIS114 4.3 15.3 1.0 CD A:GLU130 4.4 24.8 1.0 CD A:CD209 4.4 14.9 0.1 CG A:HIS114 4.7 12.8 1.0 CB A:SER118 4.8 15.8 0.5 OG A:SER118 4.9 16.5 0.5 CA A:CYS126 4.9 11.6 1.0

Iridium 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 Iridium with other atoms in the Ir binding site number 3 of Structure of Ircp* Immobilized Apo-D38H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir213 b:23.0 occ:0.20 IR1 A:RIR201 1.3 13.8 0.3 C21 A:RIR201 1.7 12.9 0.3 C20 A:RIR201 1.9 14.1 0.3 C26 A:RIR201 2.3 13.8 0.3 C17 A:RIR201 2.3 13.4 0.3 C19 A:RIR201 2.6 14.4 0.3 C25 A:RIR201 2.6 14.8 0.3 SG A:CYS48 2.8 16.0 1.0 ND1 A:HIS38 2.9 28.7 1.0 C18 A:RIR201 2.9 13.6 0.3 ND1 A:HIS49 3.2 23.2 0.7 CE1 A:HIS49 3.3 22.6 0.7 CE1 A:HIS38 3.4 29.0 1.0 C22 A:RIR201 3.4 14.0 0.3 C24 A:RIR201 4.0 15.4 0.3 CB A:CYS48 4.1 12.2 1.0 C23 A:RIR201 4.2 15.2 0.3 CG A:HIS38 4.2 23.2 1.0 CG A:HIS49 4.6 20.4 0.7 NE2 A:HIS49 4.6 25.9 0.7 NE2 A:HIS38 4.7 29.0 1.0 N A:HIS49 4.8 11.4 1.0 C A:CYS48 4.9 10.8 1.0 CB A:HIS38 4.9 18.6 1.0

Iridium 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 Iridium with other atoms in the Ir binding site number 4 of Structure of Ircp* Immobilized Apo-D38H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir214 b:26.1 occ:0.15 NE2 A:HIS173 3.4 44.7 1.0 CD2 A:HIS173 4.0 41.5 1.0 CE1 A:HIS173 4.5 43.1 1.0

Iridium 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 Iridium with other atoms in the Ir binding site number 5 of Structure of Ircp* Immobilized Apo-D38H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir215 b:34.3 occ:0.10 CE1 A:HIS49 2.2 18.8 0.3 NE2 A:HIS49 2.5 18.9 0.3 OE2 A:GLU53 2.9 34.6 0.5 ND1 A:HIS49 3.5 18.9 0.3 CD A:GLU53 3.9 23.7 0.5 CD2 A:HIS49 3.9 19.5 0.3 OE1 A:GLU53 4.3 29.2 0.5 CB A:LYS172 4.3 35.9 1.0 CG A:HIS49 4.3 16.2 0.3 CG A:GLU53 5.0 19.9 0.5

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