Iron in PDB 5opa: The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B

All present enzymatic activity of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B:
1.14.21.9;

The structure of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B, PDB code: 5opa was solved by C.W.Levy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.50 / 1.35
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.887, 77.887, 263.547, 90.00, 90.00, 120.00
R / Rfree (%)	13 / 15.7

The structure of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Iron atom in the The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B (pdb code 5opa). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B, PDB code: 5opa:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:11.3 occ:0.52 FE A:HEM404 0.0 11.3 0.5 FE A:HEM404 0.0 12.2 0.5 ND A:HEM404 2.0 11.6 0.5 ND A:HEM404 2.0 10.5 0.5 NC A:HEM404 2.0 12.3 0.5 NB A:HEM404 2.0 11.9 0.5 NB A:HEM404 2.0 9.2 0.5 NA A:HEM404 2.0 10.9 0.5 NA A:HEM404 2.1 10.1 0.5 NC A:HEM404 2.1 8.8 0.5 O A:HOH546 2.2 17.6 1.0 SG A:CYS345 2.3 13.3 1.0 C4D A:HEM404 3.0 9.3 0.5 C4C A:HEM404 3.0 12.1 0.5 C4B A:HEM404 3.0 12.3 0.5 C1D A:HEM404 3.0 11.1 0.5 C4D A:HEM404 3.0 10.0 0.5 C1C A:HEM404 3.0 12.4 0.5 C1D A:HEM404 3.0 11.2 0.5 C4B A:HEM404 3.0 7.9 0.5 C1B A:HEM404 3.1 12.3 0.5 C1B A:HEM404 3.1 8.6 0.5 C1A A:HEM404 3.1 13.5 0.5 C1C A:HEM404 3.1 9.6 0.5 C4A A:HEM404 3.1 11.3 0.5 C4A A:HEM404 3.1 8.3 0.5 C1A A:HEM404 3.1 10.2 0.5 C4C A:HEM404 3.1 9.0 0.5 CHD A:HEM404 3.4 12.2 0.5 CHC A:HEM404 3.4 12.6 0.5 CHA A:HEM404 3.4 12.7 0.5 CB A:CYS345 3.4 12.4 1.0 CHC A:HEM404 3.4 8.2 0.5 CHA A:HEM404 3.4 8.8 0.5 CHD A:HEM404 3.4 9.0 0.5 CHB A:HEM404 3.4 12.0 0.5 CHB A:HEM404 3.4 7.8 0.5 CA A:CYS345 4.2 11.7 1.0 C3D A:HEM404 4.2 9.5 0.5 C3B A:HEM404 4.2 11.8 0.5 C2D A:HEM404 4.2 11.6 0.5 C3D A:HEM404 4.2 9.7 0.5 C2B A:HEM404 4.2 12.6 0.5 C2D A:HEM404 4.2 10.8 0.5 C3C A:HEM404 4.2 11.4 0.5 C2C A:HEM404 4.3 12.7 0.5 C3B A:HEM404 4.3 8.7 0.5 C2B A:HEM404 4.3 8.9 0.5 C2C A:HEM404 4.3 10.9 0.5 C3A A:HEM404 4.3 11.2 0.5 C3A A:HEM404 4.3 9.6 0.5 C3C A:HEM404 4.3 11.2 0.5 C2A A:HEM404 4.3 13.1 0.5 C2A A:HEM404 4.3 10.9 0.5 OG A:SER237 4.5 11.2 1.0 O4 A:SO4407 4.6 29.6 0.9 CD A:PRO346 4.8 13.2 1.0 CB A:SER237 4.9 10.7 1.0 C A:CYS345 4.9 13.7 1.0 N A:GLY347 5.0 13.4 1.0

Iron binding site 2 out of 2 in the The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:12.2 occ:0.48 FE A:HEM404 0.0 12.2 0.5 FE A:HEM404 0.0 11.3 0.5 ND A:HEM404 2.0 11.6 0.5 NC A:HEM404 2.0 12.3 0.5 NB A:HEM404 2.0 11.9 0.5 ND A:HEM404 2.0 10.5 0.5 NB A:HEM404 2.0 9.2 0.5 NA A:HEM404 2.0 10.9 0.5 NC A:HEM404 2.0 8.8 0.5 NA A:HEM404 2.1 10.1 0.5 O A:HOH546 2.2 17.6 1.0 SG A:CYS345 2.3 13.3 1.0 C4B A:HEM404 3.0 12.3 0.5 C1C A:HEM404 3.0 12.4 0.5 C4C A:HEM404 3.0 12.1 0.5 C4B A:HEM404 3.0 7.9 0.5 C1D A:HEM404 3.0 11.2 0.5 C4D A:HEM404 3.0 9.3 0.5 C1B A:HEM404 3.0 12.3 0.5 C1D A:HEM404 3.0 11.1 0.5 C4D A:HEM404 3.0 10.0 0.5 C1C A:HEM404 3.1 9.6 0.5 C1B A:HEM404 3.1 8.6 0.5 C1A A:HEM404 3.1 13.5 0.5 C4C A:HEM404 3.1 9.0 0.5 C4A A:HEM404 3.1 11.3 0.5 C4A A:HEM404 3.1 8.3 0.5 C1A A:HEM404 3.1 10.2 0.5 CHC A:HEM404 3.4 12.6 0.5 CHD A:HEM404 3.4 12.2 0.5 CHC A:HEM404 3.4 8.2 0.5 CHA A:HEM404 3.4 12.7 0.5 CB A:CYS345 3.4 12.4 1.0 CHD A:HEM404 3.4 9.0 0.5 CHB A:HEM404 3.4 12.0 0.5 CHA A:HEM404 3.4 8.8 0.5 CHB A:HEM404 3.5 7.8 0.5 CA A:CYS345 4.2 11.7 1.0 C3B A:HEM404 4.2 11.8 0.5 C2B A:HEM404 4.2 12.6 0.5 C2D A:HEM404 4.2 11.6 0.5 C3D A:HEM404 4.2 9.5 0.5 C3D A:HEM404 4.2 9.7 0.5 C3C A:HEM404 4.2 11.4 0.5 C2C A:HEM404 4.3 12.7 0.5 C2D A:HEM404 4.3 10.8 0.5 C3B A:HEM404 4.3 8.7 0.5 C2B A:HEM404 4.3 8.9 0.5 C2C A:HEM404 4.3 10.9 0.5 C3C A:HEM404 4.3 11.2 0.5 C3A A:HEM404 4.3 11.2 0.5 C2A A:HEM404 4.3 13.1 0.5 C3A A:HEM404 4.3 9.6 0.5 C2A A:HEM404 4.3 10.9 0.5 OG A:SER237 4.5 11.2 1.0 O4 A:SO4407 4.6 29.6 0.9 CD A:PRO346 4.8 13.2 1.0 CB A:SER237 4.9 10.7 1.0 C A:CYS345 4.9 13.7 1.0 N A:GLY347 5.0 13.4 1.0

I.M.Taban, H.E.A.E.Elshihawy, B.Torun, B.Zucchini, C.J.Williamson, D.Altuwairigi, A.S.T.Ngu, K.J.Mclean, C.W.Levy, S.Sood, L.B.Marino, A.W.Munro, L.P.S.De Carvalho, C.Simons. Novel Aryl Substituted Pyrazoles As Small Molecule Inhibitors of Cytochrome P450 CYP121A1: Synthesis and Antimycobacterial Evaluation. J. Med. Chem. V. 60 10257 2017.
ISSN: ISSN 1520-4804
PubMed: 29185746
DOI: 10.1021/ACS.JMEDCHEM.7B01562