Iridium in PDB 5e1u: Crystal Structure of Ircp*-Apo-Fr

The structure of Crystal Structure of Ircp*-Apo-Fr, PDB code: 5e1u was solved by B.Maity, K.Fukumori, S.Abe, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.13 / 1.56
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.035, 181.035, 181.035, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 18.8

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

Cadmium

(Cd)

1 atom

The binding sites of Iridium atom in the Crystal Structure of Ircp*-Apo-Fr (pdb code 5e1u). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 7 binding sites of Iridium where determined in the Crystal Structure of Ircp*-Apo-Fr, PDB code: 5e1u:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7;

Iridium binding site 1 out of 7 in the Crystal Structure of Ircp*-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Crystal Structure of Ircp*-Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir201 b:30.6 occ:0.30 NE2 A:HIS114 2.1 27.3 1.0 CE1 A:HIS114 2.7 23.8 1.0 OE2 A:GLU130 3.3 36.2 1.0 CD2 A:HIS114 3.3 26.8 1.0 CB A:CYS126 3.6 23.2 1.0 SG A:CYS126 3.6 30.8 1.0 ND1 A:HIS114 3.9 30.1 1.0 CG A:HIS114 4.2 27.8 1.0 CB A:SER118 4.3 35.2 1.0 CD A:GLU130 4.6 39.8 1.0 OG A:SER118 4.6 42.4 1.0 O A:HOH443 4.7 30.4 1.0 CA A:CYS126 4.8 23.4 1.0

Iridium binding site 2 out of 7 in the Crystal Structure of Ircp*-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Crystal Structure of Ircp*-Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir202 b:39.1 occ:0.20 CE1 A:HIS49 2.5 37.6 1.0 IR A:IR3204 2.5 35.1 0.3 NE2 A:HIS49 2.7 29.6 1.0 IR A:IR3205 2.8 30.4 0.3 ND1 A:HIS49 3.6 34.7 1.0 CD2 A:HIS49 3.9 31.5 1.0 CD2 A:HIS173 4.2 66.5 1.0 CG A:HIS49 4.3 24.0 1.0 CG A:HIS173 4.7 65.6 1.0 NE2 A:HIS173 4.7 73.9 1.0

Iridium binding site 3 out of 7 in the Crystal Structure of Ircp*-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Crystal Structure of Ircp*-Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir203 b:35.2 occ:0.20 CD1 A:PHE128 2.1 23.2 1.0 O A:HOH308 2.8 35.1 1.0 CE1 A:PHE128 2.8 21.6 1.0 CG A:PHE128 3.2 22.3 1.0 CB A:PHE128 3.6 20.5 1.0 ND1 A:HIS132 3.6 43.6 1.0 CE1 A:HIS132 3.7 42.7 1.0 CA A:PHE128 4.1 20.5 1.0 CZ A:PHE128 4.1 21.6 1.0 O A:HOH391 4.2 30.2 1.0 O A:HOH405 4.3 33.0 1.0 CE1 A:HIS124 4.4 20.2 1.0 CD2 A:PHE128 4.4 23.8 1.0 OE1 A:GLN71 4.7 25.1 1.0 NE2 A:HIS124 4.8 20.6 1.0 CG A:MET68 4.8 15.2 1.0 CE2 A:PHE128 4.8 25.9 1.0 CG A:HIS132 5.0 36.2 1.0 C A:PHE128 5.0 22.6 1.0 O A:PHE128 5.0 21.1 1.0

Iridium binding site 4 out of 7 in the Crystal Structure of Ircp*-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Crystal Structure of Ircp*-Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir204 b:35.1 occ:0.30 IR A:IR3205 1.7 30.4 0.3 NE2 A:HIS49 2.4 29.6 1.0 CD2 A:HIS173 2.4 66.5 1.0 NE2 A:HIS173 2.4 73.9 1.0 IR A:IR3202 2.5 39.1 0.2 CE1 A:HIS49 3.3 37.6 1.0 CD2 A:HIS49 3.3 31.5 1.0 CG A:HIS173 3.3 65.6 1.0 CE1 A:HIS173 3.4 69.1 1.0 ND1 A:HIS173 3.8 65.4 1.0 ND1 A:HIS49 4.4 34.7 1.0 CB A:HIS173 4.4 60.8 1.0 CG A:HIS49 4.4 24.0 1.0 O A:HOH463 4.9 37.4 1.0

Iridium binding site 5 out of 7 in the Crystal Structure of Ircp*-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Crystal Structure of Ircp*-Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir205 b:30.4 occ:0.30 IR A:IR3204 1.7 35.1 0.3 NE2 A:HIS49 2.1 29.6 1.0 CE1 A:HIS49 2.8 37.6 1.0 IR A:IR3202 2.8 39.1 0.2 CD2 A:HIS49 3.2 31.5 1.0 NE2 A:HIS173 3.7 73.9 1.0 ND1 A:HIS49 4.0 34.7 1.0 CD2 A:HIS173 4.0 66.5 1.0 CG A:HIS49 4.2 24.0 1.0 O A:HOH463 4.2 37.4 1.0 CE1 A:HIS173 4.4 69.1 1.0 CG A:GLU53 4.5 30.0 1.0 CB A:GLU53 4.9 18.3 1.0 CG A:HIS173 4.9 65.6 1.0

Iridium binding site 6 out of 7 in the Crystal Structure of Ircp*-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Crystal Structure of Ircp*-Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir206 b:31.9 occ:0.20 CE A:LYS172 3.2 46.4 1.0 NZ A:LYS172 3.5 34.6 1.0 CD A:LYS172 4.2 37.3 1.0

Iridium binding site 7 out of 7 in the Crystal Structure of Ircp*-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Crystal Structure of Ircp*-Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir210 b:25.7 occ:0.40 IR1 A:RIR210 0.0 25.7 0.4 C17 A:RIR210 2.1 26.7 0.4 C21 A:RIR210 2.1 26.8 0.4 C18 A:RIR210 2.1 25.9 0.4 C20 A:RIR210 2.1 29.2 0.4 C19 A:RIR210 2.1 26.7 0.4 SG A:CYS48 2.4 14.7 1.0 C23 A:RIR210 3.0 27.4 0.4 C26 A:RIR210 3.1 33.6 0.4 C25 A:RIR210 3.2 31.5 0.4 O A:HOH346 3.3 27.0 1.0 C22 A:RIR210 3.3 31.9 0.4 C24 A:RIR210 3.4 27.9 0.4 CB A:CYS48 3.6 13.3 1.0 CD A:ARG52 4.3 29.7 1.0 OD1 A:ASP38 4.5 16.7 1.0 N A:HIS49 4.5 12.0 1.0 C A:CYS48 4.6 11.7 1.0 CB A:ASP38 4.7 12.0 1.0 NH2 A:ARG52 4.7 59.5 1.0 CA A:CYS48 4.7 11.6 1.0 CG A:ASP38 4.8 15.5 1.0 CG A:GLU45 4.8 25.0 1.0 O A:GLU45 4.8 13.1 1.0 CA A:HIS49 5.0 13.1 1.0 CG A:ARG52 5.0 21.6 1.0

B.Maity, K.Fukumori, S.Abe, T.Ueno. Immobilization of Two Organometallic Complexes Into A Single Cage to Construct Protein-Based Microcompartments Chem.Commun.(Camb.) V. 52 5463 2016.
ISSN: ESSN 1364-548X
PubMed: 27021005
DOI: 10.1039/C6CC00679E