Iron in PDB 5te8: Crystal Structure of the Midazolam-Bound Human CYP3A4

The structure of Crystal Structure of the Midazolam-Bound Human CYP3A4, PDB code: 5te8 was solved by I.Sevrioukova, T.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	102.34 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.289, 117.980, 205.649, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 29.2

The structure of Crystal Structure of the Midazolam-Bound Human CYP3A4 also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Iron atom in the Crystal Structure of the Midazolam-Bound Human CYP3A4 (pdb code 5te8). 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 the Midazolam-Bound Human CYP3A4, PDB code: 5te8:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of the Midazolam-Bound Human CYP3A4


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 the Midazolam-Bound Human CYP3A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:24.5 occ:1.00 FE A:HEM601 0.0 24.5 1.0 ND A:HEM601 1.9 24.5 1.0 NA A:HEM601 2.0 23.4 1.0 NB A:HEM601 2.1 23.5 1.0 NC A:HEM601 2.1 25.4 1.0 SG A:CYS442 2.4 25.1 1.0 C4D A:HEM601 2.9 24.3 1.0 C1D A:HEM601 2.9 25.3 1.0 C1A A:HEM601 2.9 23.6 1.0 C4A A:HEM601 3.0 23.0 1.0 C1B A:HEM601 3.0 23.2 1.0 C4C A:HEM601 3.1 26.2 1.0 C4B A:HEM601 3.1 24.2 1.0 C1C A:HEM601 3.2 25.7 1.0 CHA A:HEM601 3.3 23.9 1.0 CAI A:08J602 3.4 32.8 1.0 CHD A:HEM601 3.4 26.1 1.0 CAH A:08J602 3.4 33.2 1.0 CHB A:HEM601 3.4 22.9 1.0 CB A:CYS442 3.5 26.2 1.0 CHC A:HEM601 3.5 25.1 1.0 C2A A:HEM601 4.1 23.2 1.0 C3D A:HEM601 4.2 25.2 1.0 C2D A:HEM601 4.2 25.5 1.0 CA A:CYS442 4.2 26.9 1.0 C3A A:HEM601 4.2 23.2 1.0 C2B A:HEM601 4.3 23.3 1.0 C3C A:HEM601 4.3 27.2 1.0 C3B A:HEM601 4.3 24.1 1.0 C2C A:HEM601 4.3 26.6 1.0 CB A:ALA305 4.5 29.7 1.0 CAV A:08J602 4.6 33.6 1.0 CAP A:08J602 4.7 33.2 1.0 O A:ALA305 4.8 31.8 1.0 CAA A:08J602 4.9 34.8 1.0 C A:CYS442 5.0 28.0 1.0

Iron binding site 2 out of 3 in the Crystal Structure of the Midazolam-Bound Human CYP3A4


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 the Midazolam-Bound Human CYP3A4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:37.0 occ:1.00 FE B:HEM601 0.0 37.0 1.0 ND B:HEM601 1.9 37.4 1.0 NA B:HEM601 2.0 34.8 1.0 NC B:HEM601 2.1 38.4 1.0 NB B:HEM601 2.1 37.2 1.0 SG B:CYS442 2.3 34.4 1.0 C4D B:HEM601 2.9 36.0 1.0 C1D B:HEM601 2.9 38.1 1.0 C1A B:HEM601 3.0 33.8 1.0 C4C B:HEM601 3.0 39.9 1.0 C4A B:HEM601 3.0 34.7 1.0 C1B B:HEM601 3.1 36.3 1.0 C4B B:HEM601 3.1 37.4 1.0 C1C B:HEM601 3.1 39.4 1.0 CHA B:HEM601 3.3 34.6 1.0 CHD B:HEM601 3.4 39.4 1.0 CHB B:HEM601 3.5 35.4 1.0 CB B:CYS442 3.5 35.0 1.0 CAI B:08J602 3.5 42.4 1.0 CHC B:HEM601 3.5 38.5 1.0 CAH B:08J602 3.6 42.6 1.0 C3D B:HEM601 4.2 37.5 1.0 C2D B:HEM601 4.2 38.2 1.0 C2A B:HEM601 4.2 33.0 1.0 C3A B:HEM601 4.2 33.8 1.0 CA B:CYS442 4.2 35.4 1.0 C3C B:HEM601 4.2 41.5 1.0 C2C B:HEM601 4.3 41.2 1.0 C2B B:HEM601 4.3 37.7 1.0 C3B B:HEM601 4.4 38.5 1.0 CB B:ALA305 4.7 39.4 1.0 CAV B:08J602 4.7 41.2 1.0 CAA B:08J602 4.8 42.4 1.0 CD1 B:PHE435 4.8 40.0 1.0 CAP B:08J602 4.8 42.4 1.0 C B:CYS442 5.0 37.5 1.0 N B:ILE443 5.0 39.2 1.0

Iron binding site 3 out of 3 in the Crystal Structure of the Midazolam-Bound Human CYP3A4


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 the Midazolam-Bound Human CYP3A4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:63.9 occ:1.00 FE C:HEM601 0.0 63.9 1.0 ND C:HEM601 1.9 60.1 1.0 NA C:HEM601 2.0 62.0 1.0 NC C:HEM601 2.1 61.9 1.0 NB C:HEM601 2.1 63.8 1.0 SG C:CYS442 2.4 77.4 1.0 C4D C:HEM601 2.9 58.7 1.0 C1D C:HEM601 2.9 59.9 1.0 C1A C:HEM601 3.0 60.6 1.0 CAH C:08J602 3.0 95.2 1.0 C4C C:HEM601 3.0 62.5 1.0 C1B C:HEM601 3.0 65.8 1.0 C4A C:HEM601 3.1 62.9 1.0 C4B C:HEM601 3.1 64.5 1.0 C1C C:HEM601 3.1 63.0 1.0 CHA C:HEM601 3.3 58.8 1.0 CHD C:HEM601 3.4 61.6 1.0 CB C:CYS442 3.4 77.1 1.0 CHB C:HEM601 3.4 64.4 1.0 CAI C:08J602 3.5 90.5 1.0 CHC C:HEM601 3.5 63.4 1.0 CAP C:08J602 4.1 97.5 1.0 C2D C:HEM601 4.1 59.6 1.0 C3D C:HEM601 4.1 58.9 1.0 CA C:CYS442 4.2 77.5 1.0 C2A C:HEM601 4.2 61.0 1.0 C3A C:HEM601 4.2 62.7 1.0 C3C C:HEM601 4.3 63.0 1.0 C2B C:HEM601 4.3 67.5 1.0 C2C C:HEM601 4.3 63.4 1.0 C3B C:HEM601 4.3 67.2 1.0 CLAC C:08J602 4.5 0.7 1.0 CB C:ALA305 4.8 60.6 1.0 CAV C:08J602 4.8 88.1 1.0 C C:CYS442 5.0 79.6 1.0

I.F.Sevrioukova, T.L.Poulos. Structural Basis For Regiospecific Midazolam Oxidation By Human Cytochrome P450 3A4. Proc. Natl. Acad. Sci. V. 114 486 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28031486
DOI: 10.1073/PNAS.1616198114