Iron in PDB 2v0m: Crystal Structure of Human P450 3A4 in Complex with Ketoconazole

All present enzymatic activity of Crystal Structure of Human P450 3A4 in Complex with Ketoconazole:
1.14.13.67; 1.14.14.1;

The structure of Crystal Structure of Human P450 3A4 in Complex with Ketoconazole, PDB code: 2v0m was solved by T.Sjogren, M.Ekroos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	228.942, 66.363, 146.419, 90.00, 102.80, 90.00
R / Rfree (%)	21.8 / 27.1

The structure of Crystal Structure of Human P450 3A4 in Complex with Ketoconazole also contains other interesting chemical elements:

Chlorine

(Cl)

10 atoms

The binding sites of Iron atom in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole (pdb code 2v0m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole, PDB code: 2v0m:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1499 b:16.0 occ:1.00 FE A:HEM1499 0.0 16.0 1.0 NA A:HEM1499 2.0 15.5 1.0 NB A:HEM1499 2.1 15.9 1.0 N2 A:KLN1500 2.1 32.0 1.0 NC A:HEM1499 2.1 15.9 1.0 ND A:HEM1499 2.1 15.6 1.0 SG A:CYS442 2.3 19.4 1.0 C1 A:KLN1500 3.0 31.8 1.0 C1A A:HEM1499 3.0 15.3 1.0 C4A A:HEM1499 3.0 15.5 1.0 C1B A:HEM1499 3.1 15.7 1.0 C4B A:HEM1499 3.1 16.3 1.0 C2 A:KLN1500 3.1 32.5 1.0 C4D A:HEM1499 3.1 15.3 1.0 C1C A:HEM1499 3.1 15.9 1.0 C4C A:HEM1499 3.1 15.6 1.0 C1D A:HEM1499 3.1 15.9 1.0 CHA A:HEM1499 3.4 15.3 1.0 CHB A:HEM1499 3.4 15.7 1.0 CB A:CYS442 3.5 19.7 1.0 CHC A:HEM1499 3.5 15.6 1.0 CHD A:HEM1499 3.5 15.6 1.0 CA A:CYS442 4.2 19.7 1.0 N1 A:KLN1500 4.2 32.4 1.0 C3 A:KLN1500 4.2 32.4 1.0 C2A A:HEM1499 4.2 14.8 1.0 C3A A:HEM1499 4.3 14.7 1.0 C2B A:HEM1499 4.3 15.8 1.0 C3B A:HEM1499 4.3 16.7 1.0 C2C A:HEM1499 4.4 15.9 1.0 C3C A:HEM1499 4.4 15.7 1.0 C3D A:HEM1499 4.4 16.0 1.0 C2D A:HEM1499 4.4 15.6 1.0 C A:CYS442 4.8 19.9 1.0 N A:ILE443 5.0 20.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1497 b:11.0 occ:1.00 FE B:HEM1497 0.0 11.0 1.0 NB B:HEM1497 2.0 10.6 1.0 NC B:HEM1497 2.1 11.3 1.0 N2 B:KLN1498 2.1 26.7 1.0 NA B:HEM1497 2.1 10.5 1.0 ND B:HEM1497 2.1 10.8 1.0 SG B:CYS442 2.3 13.9 1.0 C1 B:KLN1498 2.9 27.4 1.0 C4B B:HEM1497 3.0 11.4 1.0 C1C B:HEM1497 3.1 11.3 1.0 C1B B:HEM1497 3.1 11.2 1.0 C4C B:HEM1497 3.1 11.5 1.0 C1A B:HEM1497 3.1 10.6 1.0 C2 B:KLN1498 3.1 26.7 1.0 C4A B:HEM1497 3.1 10.2 1.0 C1D B:HEM1497 3.1 11.2 1.0 C4D B:HEM1497 3.1 10.9 1.0 CHC B:HEM1497 3.4 11.5 1.0 CHD B:HEM1497 3.4 11.2 1.0 CHB B:HEM1497 3.5 10.9 1.0 CHA B:HEM1497 3.5 10.8 1.0 CB B:CYS442 3.6 13.1 1.0 N1 B:KLN1498 4.1 28.6 1.0 C3 B:KLN1498 4.2 27.4 1.0 CA B:CYS442 4.3 13.2 1.0 C3B B:HEM1497 4.3 11.6 1.0 C2C B:HEM1497 4.3 11.4 1.0 C2B B:HEM1497 4.3 11.8 1.0 C3C B:HEM1497 4.3 11.6 1.0 C2A B:HEM1497 4.3 10.4 1.0 C3A B:HEM1497 4.3 10.0 1.0 C2D B:HEM1497 4.3 11.4 1.0 C3D B:HEM1497 4.4 11.2 1.0 C B:CYS442 5.0 13.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1497 b:11.6 occ:1.00 FE C:HEM1497 0.0 11.6 1.0 NB C:HEM1497 2.0 11.4 1.0 NA C:HEM1497 2.0 11.2 1.0 NC C:HEM1497 2.1 10.9 1.0 N2 C:KLN1498 2.1 24.9 1.0 ND C:HEM1497 2.2 12.3 1.0 SG C:CYS442 2.3 11.2 1.0 C2 C:KLN1498 3.0 25.4 1.0 C4B C:HEM1497 3.0 11.3 1.0 C1C C:HEM1497 3.0 10.9 1.0 C1A C:HEM1497 3.0 11.7 1.0 C4A C:HEM1497 3.1 11.3 1.0 C1B C:HEM1497 3.1 11.6 1.0 C1 C:KLN1498 3.1 25.2 1.0 C4C C:HEM1497 3.1 10.5 1.0 C4D C:HEM1497 3.1 11.7 1.0 C1D C:HEM1497 3.2 12.4 1.0 CHC C:HEM1497 3.4 11.2 1.0 CHA C:HEM1497 3.4 11.4 1.0 CB C:CYS442 3.4 11.1 1.0 CHB C:HEM1497 3.4 11.4 1.0 CHD C:HEM1497 3.5 11.2 1.0 C3 C:KLN1498 4.2 25.4 1.0 N1 C:KLN1498 4.2 25.7 1.0 CA C:CYS442 4.2 11.3 1.0 C3B C:HEM1497 4.3 11.7 1.0 C2A C:HEM1497 4.3 11.1 1.0 C2C C:HEM1497 4.3 10.3 1.0 C2B C:HEM1497 4.3 11.7 1.0 C3A C:HEM1497 4.3 11.1 1.0 C3C C:HEM1497 4.3 10.1 1.0 C3D C:HEM1497 4.4 12.2 1.0 C2D C:HEM1497 4.4 12.2 1.0 C C:CYS442 5.0 11.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Human P450 3A4 in Complex with Ketoconazole within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1497 b:10.5 occ:1.00 FE D:HEM1497 0.0 10.5 1.0 NA D:HEM1497 2.0 9.6 1.0 NB D:HEM1497 2.1 8.9 1.0 NC D:HEM1497 2.1 10.6 1.0 ND D:HEM1497 2.1 9.4 1.0 N2 D:KLN1498 2.3 19.4 1.0 SG D:CYS442 2.4 12.2 1.0 C1A D:HEM1497 3.0 10.0 1.0 C4B D:HEM1497 3.1 9.6 1.0 C4A D:HEM1497 3.1 9.6 1.0 C1C D:HEM1497 3.1 10.2 1.0 C1B D:HEM1497 3.1 8.4 1.0 C4C D:HEM1497 3.1 10.8 1.0 C4D D:HEM1497 3.1 9.8 1.0 C1D D:HEM1497 3.1 10.5 1.0 C1 D:KLN1498 3.1 20.2 1.0 C2 D:KLN1498 3.3 19.4 1.0 CHC D:HEM1497 3.4 9.8 1.0 CHA D:HEM1497 3.4 9.7 1.0 CB D:CYS442 3.4 12.2 1.0 CHD D:HEM1497 3.4 10.7 1.0 CHB D:HEM1497 3.5 9.4 1.0 CA D:CYS442 4.2 12.3 1.0 C2A D:HEM1497 4.2 9.9 1.0 C3A D:HEM1497 4.3 9.7 1.0 C3B D:HEM1497 4.3 9.1 1.0 C2B D:HEM1497 4.3 8.3 1.0 C2C D:HEM1497 4.3 10.6 1.0 C3C D:HEM1497 4.3 10.9 1.0 N1 D:KLN1498 4.3 21.0 1.0 C2D D:HEM1497 4.3 9.9 1.0 C3D D:HEM1497 4.4 10.4 1.0 C3 D:KLN1498 4.4 20.0 1.0 C D:CYS442 4.9 12.8 1.0 N D:GLY444 4.9 13.6 1.0 N D:ILE443 5.0 13.1 1.0

M.Ekroos, T.Sjogren. Structural Basis For Ligand Promiscuity in Cytochrome P450 3A4 Proc.Natl.Acad.Sci.Usa V. 103 13682 2006.
ISSN: ISSN 0027-8424
PubMed: 16954191
DOI: 10.1073/PNAS.0603236103