Iron in PDB 7zxd: Crystal Structure of CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor

All present enzymatic activity of Crystal Structure of CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor:
1.14.15.29;

The structure of Crystal Structure of CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor, PDB code: 7zxd was solved by M.Snee, M.Katariya, C.Levy, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.91 / 2.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.237, 69.218, 144.14, 90, 94.35, 90
R / Rfree (%)	19.6 / 21.9

The structure of Crystal Structure of CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Crystal Structure of CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor (pdb code 7zxd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor, PDB code: 7zxd:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor


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 CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:23.6 occ:1.00 FE A:HEM503 0.0 23.6 1.0 NB A:HEM503 2.0 19.5 1.0 ND A:HEM503 2.0 24.4 1.0 NC A:HEM503 2.0 20.2 1.0 NA A:HEM503 2.1 21.3 1.0 O A:HOH605 2.3 28.7 1.0 SG A:CYS377 2.4 22.6 1.0 C1D A:HEM503 3.0 23.7 1.0 C1B A:HEM503 3.0 19.2 1.0 C4C A:HEM503 3.1 23.0 1.0 C4B A:HEM503 3.1 20.8 1.0 C4A A:HEM503 3.1 20.7 1.0 C4D A:HEM503 3.1 24.4 1.0 C1C A:HEM503 3.1 22.5 1.0 C1A A:HEM503 3.1 19.9 1.0 CB A:CYS377 3.4 20.9 1.0 CHD A:HEM503 3.4 22.8 1.0 CHB A:HEM503 3.4 19.1 1.0 CHC A:HEM503 3.4 22.1 1.0 CHA A:HEM503 3.5 23.6 1.0 N14 A:KB9502 4.0 37.5 1.0 CA A:CYS377 4.1 24.9 1.0 O A:ALA268 4.1 29.8 1.0 C2D A:HEM503 4.3 25.5 1.0 C2B A:HEM503 4.3 20.4 1.0 C3D A:HEM503 4.3 25.6 1.0 C3B A:HEM503 4.3 19.2 1.0 C3C A:HEM503 4.3 20.8 1.0 C3A A:HEM503 4.3 19.4 1.0 C2C A:HEM503 4.3 25.2 1.0 C2A A:HEM503 4.3 22.5 1.0 C15 A:KB9502 4.7 37.4 1.0 CB A:ALA268 4.7 32.3 1.0 C A:CYS377 4.8 27.3 1.0 C13 A:KB9502 4.9 30.9 1.0 N A:GLY379 4.9 26.3 1.0 C A:ALA268 4.9 27.5 1.0 N A:ILE378 5.0 26.0 1.0

Iron binding site 2 out of 3 in the Crystal Structure of CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor


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 CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:46.2 occ:1.00 FE B:HEM502 0.0 46.2 1.0 NB B:HEM502 2.0 42.3 1.0 ND B:HEM502 2.0 44.5 1.0 NC B:HEM502 2.0 45.4 1.0 NA B:HEM502 2.1 43.0 1.0 O B:HOH611 2.5 49.7 1.0 SG B:CYS377 2.6 52.9 1.0 C1B B:HEM502 3.0 40.2 1.0 C1D B:HEM502 3.0 48.7 1.0 C4A B:HEM502 3.1 42.8 1.0 C4C B:HEM502 3.1 48.8 1.0 C4B B:HEM502 3.1 45.5 1.0 C4D B:HEM502 3.1 48.3 1.0 C1C B:HEM502 3.1 49.5 1.0 C1A B:HEM502 3.1 50.1 1.0 CB B:CYS377 3.3 49.7 1.0 CHB B:HEM502 3.4 41.1 1.0 CHD B:HEM502 3.4 49.2 1.0 CHC B:HEM502 3.4 47.6 1.0 CHA B:HEM502 3.4 45.6 1.0 CA B:CYS377 4.2 53.6 1.0 C2B B:HEM502 4.3 42.9 1.0 C2D B:HEM502 4.3 54.8 1.0 C3D B:HEM502 4.3 50.3 1.0 C3B B:HEM502 4.3 40.2 1.0 C3A B:HEM502 4.3 48.0 1.0 C3C B:HEM502 4.3 51.3 1.0 C2A B:HEM502 4.3 48.0 1.0 C2C B:HEM502 4.3 48.8 1.0 O B:ALA268 4.4 54.4 1.0 N14 B:KB9501 4.4 58.8 1.0 CB B:ALA268 4.7 50.9 1.0 C13 B:KB9501 4.9 62.4 1.0 C B:CYS377 4.9 49.6 1.0 C B:ALA268 4.9 49.0 1.0 N B:GLY379 4.9 48.8 1.0

Iron binding site 3 out of 3 in the Crystal Structure of CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of CYP125 From Mycobacterium Tuberculosis in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:53.1 occ:1.00 FE C:HEM502 0.0 53.1 1.0 ND C:HEM502 2.0 55.0 1.0 NA C:HEM502 2.0 52.7 1.0 NC C:HEM502 2.0 50.7 1.0 NB C:HEM502 2.1 56.3 1.0 O C:HOH604 2.3 56.5 1.0 SG C:CYS377 2.7 56.4 1.0 C1D C:HEM502 3.0 56.8 1.0 C4A C:HEM502 3.1 56.5 1.0 C4D C:HEM502 3.1 58.7 1.0 C4C C:HEM502 3.1 54.5 1.0 C1A C:HEM502 3.1 55.2 1.0 C1C C:HEM502 3.1 52.4 1.0 C1B C:HEM502 3.1 53.4 1.0 C4B C:HEM502 3.1 52.4 1.0 CHD C:HEM502 3.4 51.9 1.0 CHB C:HEM502 3.4 53.6 1.0 CHA C:HEM502 3.4 58.8 1.0 CB C:CYS377 3.4 54.6 1.0 CHC C:HEM502 3.5 50.4 1.0 N14 C:KB9501 4.2 57.6 1.0 O C:ALA268 4.2 56.3 1.0 CA C:CYS377 4.2 58.0 1.0 C2D C:HEM502 4.3 56.1 1.0 C3D C:HEM502 4.3 62.3 1.0 C3A C:HEM502 4.3 52.6 1.0 C3C C:HEM502 4.3 52.4 1.0 C2C C:HEM502 4.3 56.5 1.0 C2A C:HEM502 4.3 56.8 1.0 C2B C:HEM502 4.3 51.6 1.0 C3B C:HEM502 4.3 53.4 1.0 C15 C:KB9501 4.8 56.9 1.0 CB C:ALA268 4.8 58.3 1.0 C C:ALA268 4.9 53.0 1.0 C C:CYS377 5.0 59.5 1.0

M.M.Katariya, M.Snee, R.B.Tunnicliffe, M.E.Kavanagh, H.I.M.Boshoff, C.N.Amadi, C.W.Levy, A.W.Munro, C.Abell, D.Leys, A.G.Coyne, K.J.Mclean. Structure Based Discovery of Inhibitors of CYP125 and CYP142 From Mycobacterium Tuberculosis. Chemistry 03868 2023.
ISSN: ISSN 0947-6539
PubMed: 36912255
DOI: 10.1002/CHEM.202203868