Iron in PDB 5wbg: Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz

The structure of Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz, PDB code: 5wbg was solved by M.B.Shah, J.R.Halpert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.293, 197.786, 119.222, 90.00, 98.51, 90.00
R / Rfree (%)	22.7 / 26.2

The structure of Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz also contains other interesting chemical elements:

Fluorine	(F)	18 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Iron atom in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz (pdb code 5wbg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz, PDB code: 5wbg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


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 Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:53.2 occ:1.00 FE A:HEM501 0.0 53.2 1.0 NA A:HEM501 1.9 42.5 1.0 ND A:HEM501 2.0 45.2 1.0 SG A:CYS436 2.0 50.9 1.0 NB A:HEM501 2.1 47.7 1.0 NC A:HEM501 2.1 58.0 1.0 C1A A:HEM501 3.0 40.9 1.0 C4D A:HEM501 3.0 43.4 1.0 C4A A:HEM501 3.0 43.2 1.0 C1D A:HEM501 3.0 49.4 1.0 C1B A:HEM501 3.1 48.8 1.0 C4C A:HEM501 3.1 58.9 1.0 C1C A:HEM501 3.1 58.6 1.0 C4B A:HEM501 3.1 52.3 1.0 CB A:CYS436 3.3 39.4 1.0 CHA A:HEM501 3.3 42.2 1.0 CHB A:HEM501 3.4 44.3 1.0 CHD A:HEM501 3.4 55.9 1.0 CHC A:HEM501 3.5 54.9 1.0 CA A:CYS436 4.1 39.8 1.0 CAA A:9ZJ502 4.1 89.4 1.0 C2A A:HEM501 4.2 38.8 1.0 C3A A:HEM501 4.2 39.5 1.0 C3D A:HEM501 4.2 38.4 1.0 C2D A:HEM501 4.3 40.2 1.0 C3C A:HEM501 4.3 56.5 1.0 C2C A:HEM501 4.3 57.4 1.0 C2B A:HEM501 4.3 45.1 1.0 C3B A:HEM501 4.3 51.5 1.0 C A:CYS436 4.9 39.7 1.0 N A:GLY438 5.0 39.6 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


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 Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:29.2 occ:1.00 FE B:HEM501 0.0 29.2 1.0 NB B:HEM501 1.9 30.6 1.0 ND B:HEM501 2.0 40.8 1.0 NA B:HEM501 2.1 35.5 1.0 SG B:CYS436 2.1 25.7 1.0 NC B:HEM501 2.2 36.7 1.0 C1B B:HEM501 3.0 31.8 1.0 C4B B:HEM501 3.0 34.8 1.0 C4D B:HEM501 3.0 40.4 1.0 C4A B:HEM501 3.1 38.1 1.0 C1D B:HEM501 3.1 37.0 1.0 C1A B:HEM501 3.1 34.0 1.0 C1C B:HEM501 3.1 38.2 1.0 C4C B:HEM501 3.2 35.8 1.0 CB B:CYS436 3.2 37.2 1.0 CHB B:HEM501 3.4 36.0 1.0 CHA B:HEM501 3.4 43.3 1.0 CHC B:HEM501 3.4 34.3 1.0 CHD B:HEM501 3.5 41.3 1.0 CA B:CYS436 4.1 35.2 1.0 C3B B:HEM501 4.2 36.0 1.0 C2B B:HEM501 4.2 32.4 1.0 CAA B:9ZJ502 4.2 0.4 1.0 C3D B:HEM501 4.3 34.0 1.0 C2D B:HEM501 4.3 26.7 1.0 C2C B:HEM501 4.3 43.0 1.0 C3A B:HEM501 4.3 38.0 1.0 C2A B:HEM501 4.3 31.5 1.0 C3C B:HEM501 4.3 38.2 1.0 N B:GLY438 4.9 39.7 1.0 C B:CYS436 5.0 35.2 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


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 Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:38.0 occ:1.00 FE C:HEM501 0.0 38.0 1.0 NA C:HEM501 1.9 29.3 1.0 NC C:HEM501 2.0 39.7 1.0 NB C:HEM501 2.0 40.7 1.0 ND C:HEM501 2.0 38.7 1.0 SG C:CYS436 2.0 38.4 1.0 C4A C:HEM501 3.0 31.2 1.0 C4C C:HEM501 3.0 42.3 1.0 C1B C:HEM501 3.0 41.1 1.0 C1D C:HEM501 3.0 38.9 1.0 C1A C:HEM501 3.0 44.5 1.0 C1C C:HEM501 3.1 38.5 1.0 C4D C:HEM501 3.1 46.4 1.0 C4B C:HEM501 3.1 37.2 1.0 CB C:CYS436 3.2 36.7 1.0 CHB C:HEM501 3.3 38.8 1.0 CHD C:HEM501 3.3 45.9 1.0 CHA C:HEM501 3.4 47.9 1.0 CHC C:HEM501 3.5 40.2 1.0 CA C:CYS436 4.0 37.9 1.0 C3A C:HEM501 4.2 34.6 1.0 C3C C:HEM501 4.2 39.9 1.0 CAA C:9ZJ502 4.2 73.3 1.0 C2A C:HEM501 4.2 40.0 1.0 C2B C:HEM501 4.2 37.0 1.0 C2D C:HEM501 4.3 37.5 1.0 C2C C:HEM501 4.3 41.8 1.0 C3B C:HEM501 4.3 40.7 1.0 C3D C:HEM501 4.3 41.2 1.0 N C:GLY438 4.8 42.1 1.0 C C:CYS436 4.8 35.9 1.0 N C:LEU437 5.0 36.5 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


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 Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:47.4 occ:1.00 FE D:HEM501 0.0 47.4 1.0 SG D:CYS436 2.1 32.8 1.0 NC D:HEM501 2.1 46.0 1.0 NB D:HEM501 2.1 51.2 1.0 ND D:HEM501 2.1 42.0 1.0 NA D:HEM501 2.1 47.7 1.0 C1C D:HEM501 3.0 55.0 1.0 C4C D:HEM501 3.0 50.7 1.0 C1D D:HEM501 3.0 42.6 1.0 C4B D:HEM501 3.1 54.8 1.0 C4D D:HEM501 3.1 44.0 1.0 C4A D:HEM501 3.1 52.9 1.0 C1B D:HEM501 3.1 52.8 1.0 C1A D:HEM501 3.1 45.5 1.0 CB D:CYS436 3.2 39.0 1.0 CHD D:HEM501 3.4 48.7 1.0 CHC D:HEM501 3.4 61.8 1.0 CHA D:HEM501 3.4 50.6 1.0 CHB D:HEM501 3.5 56.2 1.0 CA D:CYS436 4.0 41.2 1.0 C3C D:HEM501 4.2 55.7 1.0 C2C D:HEM501 4.2 56.7 1.0 CAA D:9ZJ502 4.3 82.6 1.0 C2D D:HEM501 4.3 37.8 1.0 C3D D:HEM501 4.3 35.4 1.0 C3B D:HEM501 4.3 50.5 1.0 C2B D:HEM501 4.3 49.6 1.0 C3A D:HEM501 4.3 48.1 1.0 C2A D:HEM501 4.4 43.5 1.0 N D:GLY438 4.6 40.3 1.0 N D:LEU437 4.6 38.5 1.0 C D:CYS436 4.7 41.1 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe501 b:36.5 occ:1.00 FE E:HEM501 0.0 36.5 1.0 SG E:CYS436 1.9 35.4 1.0 NB E:HEM501 2.0 36.3 1.0 NA E:HEM501 2.0 42.7 1.0 ND E:HEM501 2.1 37.6 1.0 NC E:HEM501 2.2 40.0 1.0 C1B E:HEM501 3.0 41.8 1.0 C4B E:HEM501 3.0 42.1 1.0 C4A E:HEM501 3.0 45.2 1.0 C1A E:HEM501 3.0 42.1 1.0 C4D E:HEM501 3.1 43.3 1.0 C1D E:HEM501 3.1 41.5 1.0 CB E:CYS436 3.1 41.1 1.0 C1C E:HEM501 3.2 38.1 1.0 C4C E:HEM501 3.2 35.4 1.0 CHB E:HEM501 3.4 42.1 1.0 CHA E:HEM501 3.4 49.5 1.0 CHC E:HEM501 3.5 45.0 1.0 CHD E:HEM501 3.5 41.7 1.0 CA E:CYS436 4.0 40.9 1.0 CAA E:9ZJ502 4.2 75.5 1.0 C2B E:HEM501 4.2 37.4 1.0 C3B E:HEM501 4.2 39.1 1.0 C3A E:HEM501 4.2 40.6 1.0 C2A E:HEM501 4.3 31.0 1.0 C3D E:HEM501 4.3 38.6 1.0 C2C E:HEM501 4.3 35.1 1.0 C2D E:HEM501 4.3 39.5 1.0 C3C E:HEM501 4.3 36.1 1.0 C E:CYS436 4.8 41.9 1.0 N E:GLY438 4.8 48.4 1.0 N E:LEU437 4.9 43.8 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:50.9 occ:1.00 FE F:HEM501 0.0 50.9 1.0 NA F:HEM501 1.9 48.4 1.0 ND F:HEM501 2.1 46.3 1.0 NB F:HEM501 2.1 52.0 1.0 NC F:HEM501 2.1 45.3 1.0 SG F:CYS436 2.1 34.8 1.0 C4A F:HEM501 2.9 47.8 1.0 C1D F:HEM501 3.0 49.3 1.0 C1A F:HEM501 3.0 46.5 1.0 C4C F:HEM501 3.0 43.7 1.0 C1B F:HEM501 3.0 53.5 1.0 C4D F:HEM501 3.1 44.4 1.0 C4B F:HEM501 3.1 50.6 1.0 C1C F:HEM501 3.2 49.4 1.0 CHB F:HEM501 3.3 49.5 1.0 CHD F:HEM501 3.3 49.8 1.0 CB F:CYS436 3.4 42.0 1.0 CHA F:HEM501 3.5 46.4 1.0 CHC F:HEM501 3.6 51.9 1.0 CAA F:9ZJ503 4.0 71.2 1.0 C3A F:HEM501 4.1 43.8 1.0 CA F:CYS436 4.2 42.1 1.0 C2A F:HEM501 4.2 39.1 1.0 C3C F:HEM501 4.2 49.9 1.0 C2D F:HEM501 4.3 40.0 1.0 C2B F:HEM501 4.3 49.0 1.0 C2C F:HEM501 4.3 52.0 1.0 C3B F:HEM501 4.3 45.9 1.0 C3D F:HEM501 4.4 42.9 1.0 N F:GLY438 4.9 48.2 1.0 C F:CYS436 5.0 43.5 1.0 N F:LEU437 5.0 46.0 1.0

M.B.Shah, Q.Zhang, J.R.Halpert. Crystal Structure of CYP2B6 in Complex with An Efavirenz Analog. Int J Mol Sci V. 19 2018.
ISSN: ESSN 1422-0067
PubMed: 29596329
DOI: 10.3390/IJMS19041025