Iron in PDB 6t0j: Crystal Structure of CYP124 in Complex with SQ109

All present enzymatic activity of Crystal Structure of CYP124 in Complex with SQ109:
1.14.15.14; 1.14.15.28;

The structure of Crystal Structure of CYP124 in Complex with SQ109, PDB code: 6t0j was solved by S.Bukhdruker, E.Marin, T.Varaksa, A.Gilep, N.Strushkevich, V.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.54 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.540, 75.110, 56.590, 90.00, 106.84, 90.00
R / Rfree (%)	14.8 / 18.3

The structure of Crystal Structure of CYP124 in Complex with SQ109 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Crystal Structure of CYP124 in Complex with SQ109 (pdb code 6t0j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of CYP124 in Complex with SQ109, PDB code: 6t0j:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of CYP124 in Complex with SQ109


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of CYP124 in Complex with SQ109 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:9.0 occ:0.65 FE A:HEM501 0.0 9.0 0.7 FE A:HEM501 0.1 9.8 0.3 ND A:HEM501 2.0 9.1 0.7 NA A:HEM501 2.0 9.8 0.3 NA A:HEM501 2.0 8.7 0.7 NB A:HEM501 2.0 8.4 0.7 NB A:HEM501 2.0 9.7 0.3 NC A:HEM501 2.1 9.4 0.7 ND A:HEM501 2.1 10.1 0.3 NC A:HEM501 2.1 10.1 0.3 SG A:CYS379 2.4 9.7 1.0 C4A A:HEM501 3.0 9.5 0.3 C1B A:HEM501 3.0 9.6 0.3 C1D A:HEM501 3.0 8.8 0.7 C1A A:HEM501 3.1 9.3 0.3 C1B A:HEM501 3.1 8.7 0.7 C4B A:HEM501 3.1 8.1 0.7 C4C A:HEM501 3.1 8.7 0.7 C4A A:HEM501 3.1 8.4 0.7 C1A A:HEM501 3.1 7.8 0.7 C4D A:HEM501 3.1 9.5 0.7 C1C A:HEM501 3.1 8.4 0.7 C4B A:HEM501 3.1 9.5 0.3 C4D A:HEM501 3.1 10.2 0.3 C1D A:HEM501 3.1 10.0 0.3 C1C A:HEM501 3.1 9.5 0.3 C4C A:HEM501 3.2 9.7 0.3 CB A:CYS379 3.4 9.8 1.0 CHB A:HEM501 3.4 9.6 0.3 CHD A:HEM501 3.4 8.9 0.7 CHB A:HEM501 3.5 8.6 0.7 CHA A:HEM501 3.5 9.0 0.7 CHC A:HEM501 3.5 8.3 0.7 CHA A:HEM501 3.5 9.6 0.3 CHC A:HEM501 3.5 9.7 0.3 CHD A:HEM501 3.5 10.0 0.3 CA A:CYS379 4.0 9.6 1.0 CAA A:RWZ502 4.0 12.6 0.7 CAA A:RWZ502 4.0 11.4 0.3 C3A A:HEM501 4.2 10.0 0.3 C2B A:HEM501 4.2 9.6 0.3 C2A A:HEM501 4.3 9.7 0.3 C3B A:HEM501 4.3 9.8 0.3 C3B A:HEM501 4.3 8.4 0.7 C2D A:HEM501 4.3 9.6 0.7 C2B A:HEM501 4.3 8.6 0.7 C3D A:HEM501 4.3 9.2 0.7 C2C A:HEM501 4.3 8.2 0.7 C2A A:HEM501 4.3 8.0 0.7 C3C A:HEM501 4.3 8.5 0.7 C3A A:HEM501 4.3 8.6 0.7 C3D A:HEM501 4.3 10.5 0.3 C2D A:HEM501 4.3 10.5 0.3 C2C A:HEM501 4.4 9.6 0.3 C3C A:HEM501 4.4 9.6 0.3 N A:GLY381 4.5 9.3 1.0 N A:LEU380 4.6 9.0 1.0 C A:CYS379 4.6 10.2 1.0 CA A:GLY381 4.9 9.1 1.0 CB A:ALA267 4.9 11.2 1.0

Iron binding site 2 out of 2 in the Crystal Structure of CYP124 in Complex with SQ109


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of CYP124 in Complex with SQ109 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:9.8 occ:0.35 FE A:HEM501 0.0 9.8 0.3 FE A:HEM501 0.1 9.0 0.7 ND A:HEM501 2.0 9.1 0.7 NC A:HEM501 2.0 9.4 0.7 ND A:HEM501 2.0 10.1 0.3 NB A:HEM501 2.1 9.7 0.3 NA A:HEM501 2.1 9.8 0.3 NB A:HEM501 2.1 8.4 0.7 NC A:HEM501 2.1 10.1 0.3 NA A:HEM501 2.1 8.7 0.7 SG A:CYS379 2.5 9.7 1.0 C1D A:HEM501 3.0 8.8 0.7 C4C A:HEM501 3.0 8.7 0.7 C1C A:HEM501 3.0 8.4 0.7 C1D A:HEM501 3.0 10.0 0.3 C1B A:HEM501 3.0 9.6 0.3 C4A A:HEM501 3.1 9.5 0.3 C4D A:HEM501 3.1 9.5 0.7 C4B A:HEM501 3.1 8.1 0.7 C4D A:HEM501 3.1 10.2 0.3 C4C A:HEM501 3.1 9.7 0.3 C4B A:HEM501 3.1 9.5 0.3 C1A A:HEM501 3.1 9.3 0.3 C1C A:HEM501 3.1 9.5 0.3 C1B A:HEM501 3.1 8.7 0.7 C1A A:HEM501 3.1 7.8 0.7 C4A A:HEM501 3.1 8.4 0.7 CHD A:HEM501 3.3 8.9 0.7 CHB A:HEM501 3.4 9.6 0.3 CHD A:HEM501 3.4 10.0 0.3 CHC A:HEM501 3.4 8.3 0.7 CHA A:HEM501 3.5 9.6 0.3 CHC A:HEM501 3.5 9.7 0.3 CHA A:HEM501 3.5 9.0 0.7 CB A:CYS379 3.5 9.8 1.0 CHB A:HEM501 3.5 8.6 0.7 CAA A:RWZ502 3.9 12.6 0.7 CAA A:RWZ502 4.0 11.4 0.3 CA A:CYS379 4.1 9.6 1.0 C2D A:HEM501 4.2 9.6 0.7 C3C A:HEM501 4.2 8.5 0.7 C2C A:HEM501 4.2 8.2 0.7 C3D A:HEM501 4.3 9.2 0.7 C2D A:HEM501 4.3 10.5 0.3 C2B A:HEM501 4.3 9.6 0.3 C3D A:HEM501 4.3 10.5 0.3 C3B A:HEM501 4.3 9.8 0.3 C3A A:HEM501 4.3 10.0 0.3 C3B A:HEM501 4.3 8.4 0.7 C2A A:HEM501 4.3 9.7 0.3 C3C A:HEM501 4.3 9.6 0.3 C2C A:HEM501 4.3 9.6 0.3 C2B A:HEM501 4.3 8.6 0.7 C2A A:HEM501 4.3 8.0 0.7 C3A A:HEM501 4.4 8.6 0.7 N A:GLY381 4.5 9.3 1.0 N A:LEU380 4.6 9.0 1.0 C A:CYS379 4.7 10.2 1.0 CB A:ALA267 4.8 11.2 1.0 CA A:GLY381 4.9 9.1 1.0

S.Bukhdruker, T.Varaksa, I.Grabovec, E.Marin, P.Shabunya, M.Kadukova, S.Grudinin, A.Kavaleuski, A.Gusach, A.Gilep, V.Borshchevskiy, N.Strushkevich. Hydroxylation of Antitubercular Drug Candidate, SQ109, By Mycobacterial Cytochrome P450. Int J Mol Sci V. 21 2020.
ISSN: ESSN 1422-0067
PubMed: 33081390
DOI: 10.3390/IJMS21207683