Iridium in PDB 7uor: Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.

The structure of Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin., PDB code: 7uor was solved by J.H.Pereira, B.J.Bloomer, J.F.Hartwig, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.15 / 3.16
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	190.213, 190.213, 266.773, 90, 90, 90
R / Rfree (%)	18.1 / 22.9

The structure of Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Iridium atom in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. (pdb code 7uor). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 6 binding sites of Iridium where determined in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin., PDB code: 7uor:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6;

Iridium binding site 1 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


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 Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir401 b:59.6 occ:1.00 IR A:HIR401 0.0 59.6 1.0 NB A:HIR401 2.0 55.8 1.0 NC A:HIR401 2.1 66.8 1.0 ND A:HIR401 2.1 58.1 1.0 NA A:HIR401 2.1 65.6 1.0 CH3 A:HIR401 2.2 40.0 1.0 C4B A:HIR401 3.0 56.9 1.0 C1B A:HIR401 3.0 60.1 1.0 C1C A:HIR401 3.1 62.3 1.0 C1D A:HIR401 3.1 57.2 1.0 C4C A:HIR401 3.1 57.0 1.0 C4D A:HIR401 3.1 59.5 1.0 C4A A:HIR401 3.1 55.9 1.0 C1A A:HIR401 3.1 63.8 1.0 OH A:HIR401 3.2 33.1 1.0 CHC A:HIR401 3.4 56.0 1.0 CHB A:HIR401 3.4 57.5 1.0 CHD A:HIR401 3.4 57.2 1.0 CHA A:HIR401 3.5 59.4 1.0 C3B A:HIR401 4.2 56.4 1.0 C2B A:HIR401 4.2 57.1 1.0 C3C A:HIR401 4.3 60.8 1.0 C2C A:HIR401 4.3 59.8 1.0 C2D A:HIR401 4.3 66.6 1.0 C3D A:HIR401 4.3 59.5 1.0 CA A:GLY317 4.3 65.5 1.0 C3A A:HIR401 4.3 55.1 1.0 C2A A:HIR401 4.4 54.9 1.0 N A:GLY319 4.8 70.5 1.0 CD1 A:PHE310 5.0 46.9 1.0 C A:GLY317 5.0 65.9 1.0

Iridium binding site 2 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


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 Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ir401 b:62.8 occ:1.00 IR B:HIR401 0.0 62.8 1.0 NB B:HIR401 2.0 50.7 1.0 ND B:HIR401 2.0 52.4 1.0 NC B:HIR401 2.0 61.0 1.0 NA B:HIR401 2.1 55.8 1.0 CH3 B:HIR401 2.1 45.8 1.0 C4B B:HIR401 3.0 51.1 1.0 C4D B:HIR401 3.0 52.1 1.0 C1C B:HIR401 3.0 52.7 1.0 C1D B:HIR401 3.0 54.0 1.0 C4C B:HIR401 3.1 64.2 1.0 C1B B:HIR401 3.1 50.4 1.0 OH B:HIR401 3.1 42.8 1.0 C1A B:HIR401 3.1 50.7 1.0 C4A B:HIR401 3.2 51.4 1.0 CHC B:HIR401 3.3 53.6 1.0 CHA B:HIR401 3.4 50.0 1.0 CHD B:HIR401 3.5 52.5 1.0 CHB B:HIR401 3.5 52.4 1.0 C3B B:HIR401 4.2 50.1 1.0 CA B:GLY317 4.2 61.1 1.0 C3D B:HIR401 4.3 63.1 1.0 C2D B:HIR401 4.3 68.9 1.0 C2C B:HIR401 4.3 51.2 1.0 C3C B:HIR401 4.3 53.1 1.0 C2B B:HIR401 4.3 52.1 1.0 C3A B:HIR401 4.4 49.2 1.0 C2A B:HIR401 4.4 51.7 1.0 N B:GLY319 4.8 62.4 1.0 C B:GLY317 4.9 66.2 1.0 CD1 B:PHE310 4.9 63.7 1.0 N B:LEU318 4.9 64.9 1.0

Iridium binding site 3 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


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 Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ir401 b:67.5 occ:1.00 IR C:HIR401 0.0 67.5 1.0 NB C:HIR401 2.0 66.0 1.0 ND C:HIR401 2.1 69.1 1.0 NC C:HIR401 2.1 71.4 1.0 NA C:HIR401 2.1 65.8 1.0 CH3 C:HIR401 2.1 23.4 1.0 C4B C:HIR401 3.0 67.3 1.0 C1D C:HIR401 3.1 72.7 1.0 C1C C:HIR401 3.1 68.2 1.0 C4C C:HIR401 3.1 72.5 1.0 C1A C:HIR401 3.1 64.9 1.0 C4D C:HIR401 3.1 62.2 1.0 C1B C:HIR401 3.1 56.2 1.0 OH C:HIR401 3.1 25.8 1.0 C4A C:HIR401 3.1 61.0 1.0 CHC C:HIR401 3.4 64.9 1.0 CHD C:HIR401 3.4 68.6 1.0 CHA C:HIR401 3.4 65.0 1.0 CHB C:HIR401 3.5 55.1 1.0 C3B C:HIR401 4.2 62.1 1.0 CA C:GLY317 4.2 70.9 1.0 C2D C:HIR401 4.3 75.2 1.0 C3C C:HIR401 4.3 65.8 1.0 C2B C:HIR401 4.3 56.0 1.0 C3D C:HIR401 4.3 67.8 1.0 C2A C:HIR401 4.3 53.6 1.0 C2C C:HIR401 4.3 65.2 1.0 C3A C:HIR401 4.3 57.4 1.0 N C:GLY319 4.8 73.2 1.0 CD1 C:PHE310 4.9 63.5 1.0 C C:GLY317 4.9 70.0 1.0 N C:LEU318 5.0 78.3 1.0

Iridium binding site 4 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


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 Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ir401 b:68.9 occ:1.00 IR D:HIR401 0.0 68.9 1.0 ND D:HIR401 2.0 64.1 1.0 NB D:HIR401 2.0 59.0 1.0 NA D:HIR401 2.1 62.0 1.0 NC D:HIR401 2.1 75.0 1.0 CH3 D:HIR401 2.1 25.5 1.0 C4B D:HIR401 3.0 54.5 1.0 C4D D:HIR401 3.0 64.1 1.0 C1D D:HIR401 3.0 63.4 1.0 C1B D:HIR401 3.1 64.7 1.0 C1A D:HIR401 3.1 62.9 1.0 OH D:HIR401 3.1 25.8 1.0 C1C D:HIR401 3.1 65.6 1.0 C4A D:HIR401 3.1 53.6 1.0 C4C D:HIR401 3.1 64.2 1.0 CHA D:HIR401 3.4 58.4 1.0 CHC D:HIR401 3.4 56.2 1.0 CHD D:HIR401 3.5 56.0 1.0 CHB D:HIR401 3.5 54.1 1.0 C3B D:HIR401 4.2 54.9 1.0 C3D D:HIR401 4.2 63.8 1.0 C2D D:HIR401 4.2 66.6 1.0 C2B D:HIR401 4.3 55.9 1.0 C2A D:HIR401 4.3 60.7 1.0 C3A D:HIR401 4.3 54.5 1.0 CA D:GLY317 4.3 81.3 1.0 C3C D:HIR401 4.3 55.7 1.0 C2C D:HIR401 4.3 58.0 1.0 N D:GLY319 4.8 86.8 1.0 CD1 D:PHE310 4.9 51.4 1.0 C D:GLY317 5.0 89.9 1.0

Iridium binding site 5 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


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 Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range: probe atom residue distance (Å) B Occ E:Ir401 b:81.2 occ:1.00 IR E:HIR401 0.0 81.2 1.0 ND E:HIR401 1.9 71.4 1.0 NA E:HIR401 2.0 58.8 1.0 NB E:HIR401 2.0 61.2 1.0 NC E:HIR401 2.1 82.5 1.0 CH3 E:HIR401 2.1 42.1 1.0 C4D E:HIR401 2.9 77.3 1.0 C1A E:HIR401 3.0 77.4 1.0 C4B E:HIR401 3.0 69.5 1.0 C1D E:HIR401 3.0 88.0 1.0 C4A E:HIR401 3.0 81.1 1.0 C1B E:HIR401 3.1 76.2 1.0 C1C E:HIR401 3.1 89.5 1.0 OH E:HIR401 3.1 42.0 1.0 C4C E:HIR401 3.1 83.3 1.0 CHA E:HIR401 3.3 78.7 1.0 CHC E:HIR401 3.4 76.3 1.0 CHB E:HIR401 3.5 76.0 1.0 CHD E:HIR401 3.5 73.7 1.0 C3D E:HIR401 4.2 63.7 1.0 C2A E:HIR401 4.2 58.2 1.0 C2D E:HIR401 4.2 68.2 1.0 C3A E:HIR401 4.2 56.7 1.0 C3B E:HIR401 4.2 60.9 1.0 C2B E:HIR401 4.3 56.6 1.0 CA E:GLY317 4.3 68.3 1.0 C2C E:HIR401 4.3 64.4 1.0 C3C E:HIR401 4.3 64.8 1.0 N E:GLY319 4.9 75.0 1.0 CD1 E:PHE310 4.9 57.0 1.0

Iridium binding site 6 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


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 Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range: probe atom residue distance (Å) B Occ F:Ir401 b:79.8 occ:1.00 IR F:HIR401 0.0 79.8 1.0 ND F:HIR401 2.0 62.2 1.0 NB F:HIR401 2.0 60.2 1.0 NC F:HIR401 2.1 79.7 1.0 NA F:HIR401 2.1 59.0 1.0 CH3 F:HIR401 2.1 79.5 1.0 C4B F:HIR401 3.0 60.6 1.0 C4D F:HIR401 3.0 60.2 1.0 C1D F:HIR401 3.0 72.2 1.0 C1C F:HIR401 3.0 78.7 1.0 C1B F:HIR401 3.1 68.2 1.0 OH F:HIR401 3.1 73.5 1.0 C1A F:HIR401 3.1 55.9 1.0 C4A F:HIR401 3.1 69.4 1.0 C4C F:HIR401 3.1 72.8 1.0 CHC F:HIR401 3.4 62.7 1.0 CHA F:HIR401 3.4 66.3 1.0 CHD F:HIR401 3.4 63.0 1.0 CHB F:HIR401 3.5 66.5 1.0 CA F:GLY317 4.2 72.4 1.0 C3B F:HIR401 4.2 71.1 1.0 C2D F:HIR401 4.2 81.4 1.0 C3D F:HIR401 4.2 66.5 1.0 C2B F:HIR401 4.3 62.9 1.0 C2C F:HIR401 4.3 76.0 1.0 C3C F:HIR401 4.3 73.9 1.0 C3A F:HIR401 4.3 60.7 1.0 C2A F:HIR401 4.3 54.5 1.0 C F:GLY317 4.8 91.8 1.0 N F:GLY319 4.8 88.3 1.0 N F:LEU318 4.9 98.1 1.0 CD1 F:PHE310 5.0 65.9 1.0

B.J.Bloomer, S.N.Natoli, M.Garcia-Borras, J.H.Pereira, D.B.Hu, P.D.Adams, K.N.Houk, D.S.Clark, J.F.Hartwig. Mechanistic and Structural Characterization of An Iridium-Containing Cytochrome Reveals Kinetically Relevant Cofactor Dynamics Nat Catal V. 6 39 2023.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-022-00899-9