Iridium in PDB 5od5: Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst

The structure of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst, PDB code: 5od5 was solved by A.K.Duhme-Klair, D.J.Raines, J.E.Clarke, E.V.Blagova, E.J.Dodson, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.42 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.692, 62.759, 68.195, 87.38, 76.90, 79.27
R / Rfree (%)	17.7 / 22.3

The structure of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst also contains other interesting chemical elements:

Iron

(Fe)

3 atoms

The binding sites of Iridium atom in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst (pdb code 5od5). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 8 binding sites of Iridium where determined in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst, PDB code: 5od5:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iridium binding site 1 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir402 b:46.0 occ:0.31 C6 A:9RT404 1.2 62.7 0.4 N2 A:9RT404 1.4 52.3 0.4 C5 A:9RT404 1.7 58.6 0.4 S1 A:9RT404 1.8 55.7 0.4 C4 A:9RT404 1.9 54.7 0.4 NE2 A:HIS227 2.5 32.8 0.5 CE1 A:HIS227 2.6 38.4 0.5 CE1 A:HIS227 2.7 67.5 0.0 O1 A:9RT404 2.7 51.8 0.4 C7 A:9RT404 2.7 57.9 0.4 O2 A:9RT404 2.8 54.5 0.4 C12 A:9RT404 2.8 51.4 0.4 IR1 A:RIR405 3.1 59.0 0.4 C3 A:9RT404 3.1 56.5 0.4 N3 A:9RT404 3.5 58.9 0.4 NE2 A:HIS227 3.6 67.8 0.0 ND1 A:HIS227 3.7 67.5 0.0 C8 A:9RT404 3.7 60.2 0.4 C13 A:9RT404 3.7 55.7 0.4 CD2 A:HIS227 3.8 40.8 0.5 C2 A:9RT404 3.9 57.5 0.4 ND1 A:HIS227 4.0 36.6 0.5 C20 A:RIR405 4.3 57.9 0.4 C25 A:RIR405 4.4 55.6 0.4 C19 A:RIR405 4.4 57.7 0.4 CG A:HIS227 4.5 40.1 0.5 C24 A:RIR405 4.7 54.9 0.4 C21 A:RIR405 4.7 58.8 0.4 CAQ A:95B403 4.7 53.0 1.0 C11 A:9RT404 4.8 63.5 0.4 CD2 A:HIS227 4.8 67.5 0.0 CG A:HIS227 4.8 67.5 0.0 C18 A:RIR405 4.9 57.4 0.4 C9 A:9RT404 5.0 61.1 0.4

Iridium binding site 2 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir405 b:59.0 occ:0.43 IR1 A:RIR405 0.0 59.0 0.4 NE2 A:HIS227 1.5 67.8 0.0 N3 A:9RT404 1.9 58.9 0.4 N2 A:9RT404 1.9 52.3 0.4 C19 A:RIR405 2.0 57.7 0.4 C20 A:RIR405 2.0 57.9 0.4 C21 A:RIR405 2.0 58.8 0.4 C18 A:RIR405 2.0 57.4 0.4 C17 A:RIR405 2.0 57.1 0.4 CE1 A:HIS227 2.1 67.5 0.0 NE2 A:HIS227 2.2 32.8 0.5 C7 A:9RT404 2.4 57.9 0.4 CD2 A:HIS227 2.5 40.8 0.5 C6 A:9RT404 2.5 62.7 0.4 CD2 A:HIS227 2.8 67.5 0.0 C11 A:9RT404 2.9 63.5 0.4 IR A:IR402 3.1 46.0 0.3 C24 A:RIR405 3.1 54.9 0.4 C25 A:RIR405 3.1 55.6 0.4 C26 A:RIR405 3.1 56.5 0.4 C23 A:RIR405 3.1 57.7 0.4 C22 A:RIR405 3.1 54.3 0.4 ND1 A:HIS227 3.3 67.5 0.0 S1 A:9RT404 3.4 55.7 0.4 CE1 A:HIS227 3.5 38.4 0.5 C8 A:9RT404 3.6 60.2 0.4 CG A:HIS227 3.7 67.5 0.0 O1 A:9RT404 3.7 51.8 0.4 CG A:HIS227 3.8 40.1 0.5 C10 A:9RT404 4.0 64.0 0.4 O2 A:9RT404 4.0 54.5 0.4 C9 A:9RT404 4.2 61.1 0.4 ND1 A:HIS227 4.3 36.6 0.5 OG1 A:THR226 4.6 71.7 1.0 C5 A:9RT404 4.6 58.6 0.4 C4 A:9RT404 4.8 54.7 0.4

Iridium binding site 3 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ B:Ir403 b:81.8 occ:0.16 OG1 B:THR226 2.0 99.0 1.0 CB B:THR226 3.4 0.7 1.0 O B:GLY225 4.0 0.9 1.0 N B:THR226 4.1 0.1 1.0 CG2 B:THR226 4.1 0.2 1.0 C B:GLY225 4.1 0.2 1.0 CA B:THR226 4.3 0.5 1.0 CA B:GLY225 5.0 0.1 1.0

Iridium binding site 4 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ B:Ir404 b:90.4 occ:0.16 IR B:IR405 2.0 94.5 0.2 O B:THR226 2.9 0.7 1.0 CB B:THR226 3.1 0.7 1.0 OG1 B:THR226 3.7 99.0 1.0 C B:THR226 3.8 0.8 1.0 CG2 B:THR226 3.8 0.2 1.0 CA B:THR226 4.0 0.5 1.0 ND1 B:HIS227 4.5 0.5 1.0

Iridium binding site 5 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ B:Ir405 b:94.5 occ:0.21 IR B:IR404 2.0 90.4 0.2 O B:THR226 2.8 0.7 1.0 ND1 B:HIS227 3.1 0.5 1.0 CE1 B:HIS227 3.4 0.5 1.0 C B:THR226 4.0 0.8 1.0 CG B:HIS227 4.2 0.7 1.0 CB B:THR226 4.5 0.7 1.0 NE2 B:HIS227 4.5 0.5 1.0 CA B:THR226 4.8 0.5 1.0 CB B:HIS227 4.9 0.1 1.0 N B:HIS227 5.0 0.8 1.0

Iridium binding site 6 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ C:Ir402 b:52.8 occ:0.17 C4 C:9RT405 1.4 42.7 0.6 C5 C:9RT405 1.5 41.6 0.6 S1 C:9RT405 1.9 43.8 0.6 N2 C:9RT405 2.0 38.2 0.6 C6 C:9RT405 2.5 36.7 0.6 O1 C:9RT405 2.6 41.7 0.6 C3 C:9RT405 2.6 39.7 0.6 C12 C:9RT405 2.7 38.0 0.6 O2 C:9RT405 3.2 43.8 0.6 CE1 C:HIS227 3.3 70.0 1.0 C7 C:9RT405 3.5 33.6 0.6 C2 C:9RT405 3.5 36.8 0.6 NE2 C:HIS227 3.5 68.8 1.0 C13 C:9RT405 3.5 34.6 0.6 IR1 C:RIR406 3.8 43.6 0.6 ND1 C:HIS227 4.1 74.1 1.0 N3 C:9RT405 4.1 28.2 0.6 C8 C:9RT405 4.3 33.1 0.6 CD2 C:HIS227 4.5 70.8 1.0 CG C:HIS227 4.8 73.5 1.0 C1 C:9RT405 4.9 38.9 0.6 C20 C:RIR406 5.0 49.3 0.6 C19 C:RIR406 5.0 45.6 0.6

Iridium binding site 7 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ C:Ir403 b:66.0 occ:0.44 ND1 C:HIS227 2.3 74.1 1.0 CE1 C:HIS227 3.0 70.0 1.0 CG C:HIS227 3.4 73.5 1.0 CB C:HIS227 3.8 67.0 1.0 NE2 C:HIS227 4.2 68.8 1.0 CD2 C:HIS227 4.3 70.8 1.0

Iridium binding site 8 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ C:Ir406 b:43.6 occ:0.63 IR1 C:RIR406 0.0 43.6 0.6 C18 C:RIR406 2.0 49.1 0.6 C17 C:RIR406 2.0 49.7 0.6 N2 C:9RT405 2.0 38.2 0.6 C21 C:RIR406 2.0 53.3 0.6 C19 C:RIR406 2.0 45.6 0.6 C20 C:RIR406 2.0 49.3 0.6 N3 C:9RT405 2.1 28.2 0.6 NE2 C:HIS227 2.2 68.8 1.0 C6 C:9RT405 2.8 36.7 0.6 C7 C:9RT405 2.8 33.6 0.6 C11 C:9RT405 3.1 35.4 0.6 C22 C:RIR406 3.1 54.4 0.6 C26 C:RIR406 3.1 51.1 0.6 C25 C:RIR406 3.2 44.8 0.6 CD2 C:HIS227 3.2 70.8 1.0 C23 C:RIR406 3.2 53.2 0.6 C24 C:RIR406 3.2 52.9 0.6 CE1 C:HIS227 3.2 70.0 1.0 S1 C:9RT405 3.4 43.8 0.6 O1 C:9RT405 3.5 41.7 0.6 IR C:IR402 3.8 52.8 0.2 O2 C:9RT405 4.0 43.8 0.6 C8 C:9RT405 4.2 33.1 0.6 ND1 C:HIS227 4.3 74.1 1.0 CG C:HIS227 4.3 73.5 1.0 C10 C:9RT405 4.4 35.3 0.6 C5 C:9RT405 4.7 41.6 0.6 C9 C:9RT405 4.8 33.1 0.6

A.D.J.Raines, J.E.Clarke, E.Blagova, E.J.Dodson, K.S.Wilson, A.K.Duhme-Klair. Redox-Switchable Siderophore Anchor Enables Reversible Artificial Metalloenzyme Assembly Nat Catal 2018.
DOI: 10.1038/S41929-018-0124-3