Iron in PDB 2zyl: Crystal Structure of 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis

The structure of Crystal Structure of 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis, PDB code: 2zyl was solved by I.D'angelo, J.Capyk, N.Strynadka, L.Eltis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 2.30
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.200, 116.200, 81.000, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 23.5

The structure of Crystal Structure of 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iron atom in the Crystal Structure of 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis (pdb code 2zyl). 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 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis, PDB code: 2zyl:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis


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 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe451 b:26.9 occ:1.00 FE1 A:FES451 0.0 26.9 1.0 ND1 A:HIS89 2.0 23.4 1.0 ND1 A:HIS69 2.1 16.9 1.0 S2 A:FES451 2.2 29.6 1.0 S1 A:FES451 2.3 30.1 1.0 FE2 A:FES451 2.8 29.8 1.0 CE1 A:HIS89 3.0 23.9 1.0 CE1 A:HIS69 3.0 18.9 1.0 CG A:HIS89 3.0 23.9 1.0 CG A:HIS69 3.2 19.6 1.0 CB A:HIS89 3.4 23.8 1.0 CB A:HIS69 3.6 23.1 1.0 N A:HIS89 3.9 25.6 1.0 NE2 A:HIS89 4.1 25.0 1.0 CD2 A:HIS89 4.2 18.3 1.0 CB A:PHE88 4.2 25.1 1.0 NE2 A:HIS69 4.2 20.0 1.0 CA A:HIS89 4.3 24.8 1.0 CD2 A:HIS69 4.3 16.8 1.0 SG A:CYS67 4.4 22.8 1.0 N A:MET70 4.4 26.3 1.0 CD2 A:PHE88 4.4 27.4 1.0 NE1 A:TRP91 4.4 21.4 1.0 CD1 A:TRP91 4.5 17.4 1.0 CG A:PHE88 4.5 24.8 1.0 SG A:CYS86 4.5 28.7 1.0 C A:PHE88 4.6 25.8 1.0 CB A:MET70 4.7 26.5 1.0 CA A:HIS69 4.7 25.2 1.0 CE2 A:TRP91 4.8 19.1 1.0 CG A:TRP91 4.8 22.2 1.0 CA A:PHE88 4.9 26.3 1.0 C A:HIS69 5.0 26.1 1.0 CD2 A:TRP91 5.0 19.1 1.0 C A:HIS89 5.0 25.4 1.0 CG A:MET70 5.0 29.6 1.0

Iron binding site 2 out of 3 in the Crystal Structure of 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis


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 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe451 b:29.8 occ:1.00 FE2 A:FES451 0.0 29.8 1.0 S1 A:FES451 2.2 30.1 1.0 SG A:CYS67 2.2 22.8 1.0 S2 A:FES451 2.3 29.6 1.0 SG A:CYS86 2.3 28.7 1.0 FE1 A:FES451 2.8 26.9 1.0 CB A:CYS67 2.9 24.4 1.0 CB A:CYS86 3.1 29.1 1.0 CB A:HIS69 4.2 23.1 1.0 CB A:PHE88 4.3 25.1 1.0 ND1 A:HIS69 4.4 16.9 1.0 CA A:CYS67 4.4 24.5 1.0 N A:GLY72 4.4 29.0 1.0 CA A:CYS86 4.5 29.0 1.0 ND1 A:HIS89 4.6 23.4 1.0 CA A:GLY72 4.6 29.0 1.0 N A:HIS89 4.7 25.6 1.0 CG A:HIS69 4.8 19.6 1.0 N A:PHE88 4.9 28.8 1.0 N A:MET70 4.9 26.3 1.0 N A:HIS69 4.9 25.5 1.0 C A:CYS67 4.9 24.4 1.0 CB A:TRP91 5.0 23.7 1.0 CD2 A:LEU74 5.0 25.6 1.0

Iron binding site 3 out of 3 in the Crystal Structure of 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis


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 3-Ketosteroid-9-Alpha-Hydroxylase (Ksha) From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe452 b:34.5 occ:1.00 O A:HOH561 2.1 34.9 1.0 NE2 A:HIS186 2.1 40.1 1.0 OD1 A:ASP304 2.1 43.2 1.0 NE2 A:HIS181 2.2 19.6 1.0 OD2 A:ASP304 2.5 45.2 1.0 CG A:ASP304 2.7 39.7 1.0 CD2 A:HIS181 3.0 22.6 1.0 CD2 A:HIS186 3.1 36.4 1.0 CE1 A:HIS186 3.2 36.2 1.0 CE1 A:HIS181 3.2 22.7 1.0 OD1 A:ASN175 4.0 39.9 1.0 CB A:ASP304 4.2 38.6 1.0 CG A:HIS186 4.2 34.9 1.0 CG A:HIS181 4.2 19.2 1.0 ND1 A:HIS186 4.2 31.4 1.0 ND1 A:HIS181 4.3 22.0 1.0 CE1 A:PHE182 4.4 28.8 1.0 CZ A:PHE182 4.5 27.0 1.0 CG A:ASN175 5.0 39.6 1.0

J.K.Capyk, I.D'angelo, N.C.Strynadka, L.D.Eltis. Characterization of 3-Ketosteroid 9{Alpha}-Hydroxylase, A Rieske Oxygenase in the Cholesterol Degradation Pathway of Mycobacterium Tuberculosis J.Biol.Chem. V. 284 9937 2009.
ISSN: ISSN 0021-9258
PubMed: 19234303
DOI: 10.1074/JBC.M900719200