Nickel 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:

Iridium

(Ir)

6 atoms

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin., PDB code: 7uor:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 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 Nickel with other atoms in the Ni 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:Ni403 b:45.6 occ:1.00 NE2 C:HIS-10 2.0 44.9 1.0 NE2 A:HIS-10 2.1 46.0 1.0 NE2 B:HIS-10 2.1 46.0 1.0 NE2 C:HIS-8 2.2 41.1 1.0 NE2 A:HIS-8 2.3 38.1 1.0 NE2 B:HIS-8 2.3 44.8 1.0 CE1 A:HIS-10 2.4 50.5 1.0 CE1 B:HIS-10 2.5 43.5 1.0 CE1 C:HIS-10 2.9 49.1 1.0 CE1 C:HIS-8 3.0 49.3 1.0 CD2 C:HIS-10 3.1 47.5 1.0 CD2 A:HIS-8 3.1 41.6 1.0 CE1 B:HIS-8 3.2 62.2 1.0 CD2 C:HIS-8 3.3 45.1 1.0 CE1 A:HIS-8 3.3 52.0 1.0 CD2 B:HIS-8 3.3 48.1 1.0 CD2 B:HIS-10 3.4 48.3 1.0 CD2 A:HIS-10 3.4 50.4 1.0 ND1 A:HIS-10 3.7 53.5 1.0 ND1 B:HIS-10 3.8 44.4 1.0 ND1 C:HIS-10 4.1 47.7 1.0 ND1 C:HIS-8 4.2 63.4 1.0 CG C:HIS-10 4.2 52.6 1.0 CG A:HIS-10 4.2 60.0 1.0 CG B:HIS-10 4.3 57.9 1.0 ND1 B:HIS-8 4.3 74.0 1.0 CG C:HIS-8 4.3 53.3 1.0 CG A:HIS-8 4.3 57.6 1.0 ND1 A:HIS-8 4.4 60.6 1.0 CG B:HIS-8 4.4 59.6 1.0

Nickel binding site 2 out of 2 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 Nickel with other atoms in the Ni 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 D:Ni403 b:48.5 occ:1.00 NE2 D:HIS-10 2.1 51.1 1.0 NE2 F:HIS-8 2.1 62.8 1.0 NE2 F:HIS-10 2.3 62.8 1.0 NE2 E:HIS-10 2.3 65.5 1.0 NE2 D:HIS-8 2.4 61.0 1.0 NE2 E:HIS-8 2.5 72.0 1.0 CE1 D:HIS-10 2.7 51.0 1.0 CE1 F:HIS-10 2.7 62.9 1.0 CE1 E:HIS-10 2.9 80.0 1.0 CE1 F:HIS-8 3.0 66.2 1.0 CE1 D:HIS-8 3.1 73.8 1.0 CE1 E:HIS-8 3.2 74.2 1.0 CD2 F:HIS-8 3.2 68.8 1.0 CD2 D:HIS-10 3.3 65.8 1.0 CD2 D:HIS-8 3.4 62.4 1.0 CD2 E:HIS-10 3.6 79.7 1.0 CD2 F:HIS-10 3.6 67.3 1.0 CD2 E:HIS-8 3.6 81.5 1.0 ND1 D:HIS-10 3.9 56.8 1.0 ND1 F:HIS-10 4.0 66.8 1.0 ND1 F:HIS-8 4.1 75.0 1.0 ND1 E:HIS-10 4.1 102.3 1.0 ND1 D:HIS-8 4.2 74.0 1.0 CG F:HIS-8 4.2 72.2 1.0 CG D:HIS-10 4.3 71.6 1.0 ND1 E:HIS-8 4.3 78.7 1.0 CG D:HIS-8 4.4 67.8 1.0 CG F:HIS-10 4.4 82.0 1.0 CG E:HIS-10 4.5 94.7 1.0 CG E:HIS-8 4.6 80.9 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