Iron in PDB 7q9e: CYP106A1

The structure of CYP106A1, PDB code: 7q9e was solved by Y.Carius, M.Hutter, F.Kiss, R.Bernhardt, C.R.D.Lancaster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.82 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.69, 82.87, 84.86, 95.36, 90, 90
R / Rfree (%)	16.9 / 20.6

The structure of CYP106A1 also contains other interesting chemical elements:

Cobalt

(Co)

3 atoms

The binding sites of Iron atom in the CYP106A1 (pdb code 7q9e). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the CYP106A1, PDB code: 7q9e:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the CYP106A1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of CYP106A1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:11.8 occ:1.00 FE A:HEM501 0.0 11.8 1.0 ND A:HEM501 2.0 12.3 1.0 NA A:HEM501 2.0 11.7 1.0 NB A:HEM501 2.1 10.9 1.0 NC A:HEM501 2.1 12.0 1.0 SG A:CYS356 2.3 12.4 1.0 O A:HOH663 2.4 25.8 1.0 C1D A:HEM501 3.0 13.8 1.0 C4D A:HEM501 3.0 12.5 1.0 C1A A:HEM501 3.0 13.4 1.0 C4B A:HEM501 3.0 10.7 1.0 C1B A:HEM501 3.1 11.8 1.0 C4C A:HEM501 3.1 12.5 1.0 C4A A:HEM501 3.1 11.9 1.0 C1C A:HEM501 3.1 11.0 1.0 CB A:CYS356 3.4 11.3 1.0 CHA A:HEM501 3.4 11.6 1.0 CHD A:HEM501 3.4 12.8 1.0 CHC A:HEM501 3.4 11.3 1.0 CHB A:HEM501 3.5 11.5 1.0 CA A:CYS356 4.0 10.9 1.0 O A:ALA244 4.2 17.8 1.0 C2D A:HEM501 4.3 13.0 1.0 C2A A:HEM501 4.3 13.7 1.0 C2B A:HEM501 4.3 10.4 1.0 C2C A:HEM501 4.3 11.8 1.0 C3A A:HEM501 4.3 12.7 1.0 C3D A:HEM501 4.3 12.5 1.0 C3C A:HEM501 4.3 12.5 1.0 C3B A:HEM501 4.3 11.0 1.0 CB A:ALA244 4.6 16.7 1.0 N A:GLY358 4.6 11.4 1.0 C A:CYS356 4.7 10.7 1.0 N A:LEU357 4.8 10.6 1.0 C A:ALA244 4.9 15.9 1.0 CA A:GLY358 4.9 12.9 1.0

Iron binding site 2 out of 4 in the CYP106A1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of CYP106A1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:10.8 occ:1.00 FE B:HEM501 0.0 10.8 1.0 ND B:HEM501 2.0 10.0 1.0 NA B:HEM501 2.0 9.7 1.0 NC B:HEM501 2.0 9.8 1.0 NB B:HEM501 2.0 9.3 1.0 O B:HOH708 2.2 22.7 1.0 SG B:CYS356 2.3 10.9 1.0 C1D B:HEM501 3.0 10.9 1.0 C4D B:HEM501 3.0 10.9 1.0 C4B B:HEM501 3.0 9.4 1.0 C1B B:HEM501 3.0 10.1 1.0 C1A B:HEM501 3.0 11.0 1.0 C4C B:HEM501 3.0 11.3 1.0 C1C B:HEM501 3.1 9.6 1.0 C4A B:HEM501 3.1 10.8 1.0 CHA B:HEM501 3.4 10.9 1.0 CB B:CYS356 3.4 10.0 1.0 CHD B:HEM501 3.4 11.0 1.0 CHC B:HEM501 3.4 10.1 1.0 CHB B:HEM501 3.4 10.6 1.0 CA B:CYS356 4.0 9.8 1.0 O B:ALA244 4.1 17.2 1.0 C2D B:HEM501 4.2 10.9 1.0 C2B B:HEM501 4.2 10.4 1.0 C3D B:HEM501 4.2 10.9 1.0 C3C B:HEM501 4.3 10.5 1.0 C3A B:HEM501 4.3 11.4 1.0 C3B B:HEM501 4.3 10.7 1.0 C2C B:HEM501 4.3 10.6 1.0 C2A B:HEM501 4.3 11.7 1.0 O2 B:PEG506 4.5 56.7 1.0 O4 B:PEG506 4.5 50.6 1.0 CB B:ALA244 4.6 14.0 1.0 N B:GLY358 4.7 12.0 1.0 C B:CYS356 4.7 10.4 1.0 N B:LEU357 4.8 11.9 1.0 C B:ALA244 4.9 14.9 1.0 CA B:GLY358 5.0 12.7 1.0

Iron binding site 3 out of 4 in the CYP106A1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of CYP106A1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:14.2 occ:1.00 FE C:HEM501 0.0 14.2 1.0 ND C:HEM501 2.0 15.1 1.0 NA C:HEM501 2.0 14.3 1.0 NB C:HEM501 2.1 14.7 1.0 NC C:HEM501 2.1 13.6 1.0 O C:HOH720 2.2 24.0 1.0 SG C:CYS356 2.3 13.1 1.0 C4D C:HEM501 3.0 16.8 1.0 C1A C:HEM501 3.0 15.9 1.0 C1D C:HEM501 3.0 15.1 1.0 C1B C:HEM501 3.0 14.5 1.0 C4A C:HEM501 3.1 15.0 1.0 C4B C:HEM501 3.1 15.0 1.0 C4C C:HEM501 3.1 14.3 1.0 C1C C:HEM501 3.1 14.3 1.0 CHA C:HEM501 3.4 15.5 1.0 CB C:CYS356 3.4 12.7 1.0 CHD C:HEM501 3.4 14.8 1.0 CHB C:HEM501 3.4 14.1 1.0 CHC C:HEM501 3.5 13.3 1.0 CA C:CYS356 4.0 13.4 1.0 O C:ALA244 4.2 22.6 1.0 C2A C:HEM501 4.2 15.9 1.0 C3D C:HEM501 4.3 16.1 1.0 C2B C:HEM501 4.3 13.9 1.0 C3A C:HEM501 4.3 15.2 1.0 C2D C:HEM501 4.3 16.6 1.0 C3C C:HEM501 4.3 14.9 1.0 C2C C:HEM501 4.3 14.5 1.0 C3B C:HEM501 4.3 14.0 1.0 N C:GLY358 4.6 12.6 1.0 N C:LEU357 4.7 15.1 1.0 C C:CYS356 4.7 13.9 1.0 CB C:ALA244 4.8 18.9 1.0 O1 C:PEG505 5.0 49.9 1.0 C2 C:PEG505 5.0 52.5 1.0 CA C:GLY358 5.0 12.2 1.0 C C:ALA244 5.0 18.5 1.0

Iron binding site 4 out of 4 in the CYP106A1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of CYP106A1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:13.0 occ:1.00 FE D:HEM501 0.0 13.0 1.0 ND D:HEM501 1.9 13.2 1.0 NA D:HEM501 2.0 12.4 1.0 NB D:HEM501 2.1 12.9 1.0 NC D:HEM501 2.1 12.6 1.0 O D:HOH708 2.1 23.4 1.0 SG D:CYS356 2.2 12.7 1.0 C4D D:HEM501 2.9 14.5 1.0 C1D D:HEM501 3.0 13.6 1.0 C1A D:HEM501 3.0 15.0 1.0 C1B D:HEM501 3.0 13.6 1.0 C4A D:HEM501 3.0 13.2 1.0 C4C D:HEM501 3.0 13.5 1.0 C4B D:HEM501 3.1 13.6 1.0 C1C D:HEM501 3.1 13.5 1.0 CHA D:HEM501 3.4 13.5 1.0 CB D:CYS356 3.4 12.6 1.0 CHB D:HEM501 3.4 12.9 1.0 CHD D:HEM501 3.4 13.3 1.0 CHC D:HEM501 3.5 13.0 1.0 CA D:CYS356 4.1 12.6 1.0 C3D D:HEM501 4.2 14.9 1.0 C2D D:HEM501 4.2 15.0 1.0 C3A D:HEM501 4.2 13.6 1.0 C3C D:HEM501 4.2 15.1 1.0 C2A D:HEM501 4.2 15.5 1.0 O D:ALA244 4.3 18.8 1.0 C2B D:HEM501 4.3 13.2 1.0 C2C D:HEM501 4.3 13.6 1.0 C3B D:HEM501 4.3 13.5 1.0 N D:GLY358 4.6 13.6 1.0 C D:CYS356 4.7 12.6 1.0 N D:LEU357 4.8 14.4 1.0 CB D:ALA244 4.8 18.8 1.0

Y.Carius, M.Hutter, F.Kiss, R.Bernhardt, C.R.D.Lancaster. Structural Comparison of the Cytochrome P450 Enzymes CYP106A1 and CYP106A2 Provides Insight Into Their Differences in Steroid Conversion. Febs Lett. V. 596 3133 2022.
ISSN: ISSN 0014-5793
PubMed: 36151590
DOI: 10.1002/1873-3468.14502