Iron in PDB 5e58: Crystal Structure of Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole

The structure of Crystal Structure of Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole, PDB code: 5e58 was solved by M.B.Shah, C.D.Stout, J.R.Halpert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	98.079, 106.066, 106.198, 64.61, 82.53, 69.93
R / Rfree (%)	21.6 / 28.3

The structure of Crystal Structure of Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Iron atom in the Crystal Structure of Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole (pdb code 5e58). 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 Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole, PDB code: 5e58:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole


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 Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:16.7 occ:1.00 FE A:HEM501 0.0 16.7 1.0 NB A:HEM501 1.8 14.1 1.0 NA A:HEM501 1.9 15.7 1.0 ND A:HEM501 2.0 15.4 1.0 N1 A:CPZ502 2.0 31.9 1.0 NC A:HEM501 2.0 18.2 1.0 SG A:CYS436 2.4 22.7 1.0 C4B A:HEM501 2.8 19.0 1.0 C1B A:HEM501 2.9 18.5 1.0 C5 A:CPZ502 2.9 33.0 1.0 C4A A:HEM501 2.9 15.5 1.0 C1A A:HEM501 2.9 16.1 1.0 C4D A:HEM501 3.0 18.8 1.0 C1C A:HEM501 3.0 18.5 1.0 C1D A:HEM501 3.1 16.2 1.0 C4C A:HEM501 3.1 14.6 1.0 C2 A:CPZ502 3.1 33.5 1.0 CB A:CYS436 3.3 17.9 1.0 CHB A:HEM501 3.3 18.2 1.0 CHC A:HEM501 3.3 19.1 1.0 CHA A:HEM501 3.3 17.1 1.0 CHD A:HEM501 3.4 12.4 1.0 C3B A:HEM501 4.0 17.9 1.0 C2B A:HEM501 4.1 18.1 1.0 CA A:CYS436 4.1 18.3 1.0 C3A A:HEM501 4.1 16.0 1.0 C2A A:HEM501 4.1 18.1 1.0 N3 A:CPZ502 4.1 33.0 1.0 C2C A:HEM501 4.2 22.3 1.0 C3D A:HEM501 4.2 14.7 1.0 C3C A:HEM501 4.2 20.9 1.0 C4 A:CPZ502 4.3 31.6 1.0 C2D A:HEM501 4.3 16.0 1.0 N A:GLY438 4.6 18.8 1.0 N A:LEU437 4.7 24.2 1.0 C A:CYS436 4.7 24.4 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole


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 Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:34.6 occ:1.00 FE B:HEM501 0.0 34.6 1.0 NB B:HEM501 1.9 34.4 1.0 N1 B:CPZ502 2.0 42.9 1.0 ND B:HEM501 2.0 35.2 1.0 NA B:HEM501 2.1 37.5 1.0 NC B:HEM501 2.1 35.2 1.0 SG B:CYS436 2.4 39.0 1.0 C5 B:CPZ502 2.9 40.6 1.0 C1B B:HEM501 3.0 37.0 1.0 C4B B:HEM501 3.0 36.9 1.0 C4D B:HEM501 3.0 37.9 1.0 C4A B:HEM501 3.1 36.3 1.0 C1A B:HEM501 3.1 38.2 1.0 C2 B:CPZ502 3.1 40.4 1.0 C1D B:HEM501 3.1 36.3 1.0 C1C B:HEM501 3.1 33.9 1.0 C4C B:HEM501 3.1 36.5 1.0 CHB B:HEM501 3.4 37.6 1.0 CHC B:HEM501 3.4 36.8 1.0 CHA B:HEM501 3.4 37.8 1.0 CB B:CYS436 3.4 45.0 1.0 CHD B:HEM501 3.5 36.3 1.0 N3 B:CPZ502 4.1 41.1 1.0 C2B B:HEM501 4.2 36.9 1.0 C3B B:HEM501 4.2 33.4 1.0 C4 B:CPZ502 4.2 39.8 1.0 CA B:CYS436 4.2 40.0 1.0 C3D B:HEM501 4.3 35.0 1.0 C3A B:HEM501 4.3 37.0 1.0 C2A B:HEM501 4.3 37.3 1.0 C2D B:HEM501 4.3 34.5 1.0 C2C B:HEM501 4.3 34.3 1.0 C3C B:HEM501 4.3 36.3 1.0 C B:CYS436 4.9 38.6 1.0 N B:LEU437 5.0 44.6 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole


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 Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:24.8 occ:1.00 FE C:HEM501 0.0 24.8 1.0 NB C:HEM501 1.9 24.6 1.0 NC C:HEM501 2.0 26.6 1.0 NA C:HEM501 2.0 23.6 1.0 N1 C:CPZ502 2.0 42.6 1.0 ND C:HEM501 2.1 20.5 1.0 SG C:CYS436 2.5 29.1 1.0 C5 C:CPZ502 3.0 44.5 1.0 C4B C:HEM501 3.0 28.6 1.0 C1B C:HEM501 3.0 23.7 1.0 C1C C:HEM501 3.0 29.8 1.0 C4A C:HEM501 3.0 23.3 1.0 C4C C:HEM501 3.0 24.6 1.0 C1A C:HEM501 3.1 25.2 1.0 C1D C:HEM501 3.1 21.4 1.0 C4D C:HEM501 3.1 22.3 1.0 C2 C:CPZ502 3.1 42.1 1.0 CHB C:HEM501 3.3 24.7 1.0 CHC C:HEM501 3.4 28.3 1.0 CHD C:HEM501 3.4 22.4 1.0 CHA C:HEM501 3.5 25.1 1.0 CB C:CYS436 3.5 31.1 1.0 N3 C:CPZ502 4.2 45.2 1.0 C2C C:HEM501 4.2 29.1 1.0 C3B C:HEM501 4.2 25.1 1.0 C3C C:HEM501 4.2 28.2 1.0 C2B C:HEM501 4.2 25.9 1.0 C4 C:CPZ502 4.3 42.1 1.0 CA C:CYS436 4.3 32.4 1.0 C3A C:HEM501 4.3 24.5 1.0 C2A C:HEM501 4.3 23.8 1.0 C2D C:HEM501 4.3 19.9 1.0 C3D C:HEM501 4.3 18.3 1.0 N C:GLY438 4.8 35.5 1.0 C C:CYS436 4.9 32.3 1.0 N C:LEU437 4.9 35.5 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole


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 Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:29.4 occ:1.00 FE D:HEM501 0.0 29.4 1.0 NC D:HEM501 2.0 32.0 1.0 ND D:HEM501 2.0 31.6 1.0 NB D:HEM501 2.0 30.0 1.0 NA D:HEM501 2.1 31.8 1.0 N1 D:CPZ503 2.1 35.6 1.0 SG D:CYS436 2.4 36.0 1.0 C4B D:HEM501 3.0 30.2 1.0 C1D D:HEM501 3.0 33.2 1.0 C1C D:HEM501 3.0 29.6 1.0 C4D D:HEM501 3.0 30.5 1.0 C4C D:HEM501 3.0 32.7 1.0 C1A D:HEM501 3.1 29.8 1.0 C5 D:CPZ503 3.1 38.6 1.0 C2 D:CPZ503 3.1 39.2 1.0 C4A D:HEM501 3.1 31.8 1.0 C1B D:HEM501 3.1 32.6 1.0 CB D:CYS436 3.3 41.4 1.0 CHC D:HEM501 3.4 29.4 1.0 CHD D:HEM501 3.4 32.5 1.0 CHA D:HEM501 3.4 30.2 1.0 CHB D:HEM501 3.5 30.4 1.0 CA D:CYS436 4.1 37.1 1.0 C2D D:HEM501 4.2 31.8 1.0 C2C D:HEM501 4.3 31.0 1.0 C3D D:HEM501 4.3 33.7 1.0 C3C D:HEM501 4.3 30.2 1.0 N3 D:CPZ503 4.3 37.5 1.0 C3B D:HEM501 4.3 33.6 1.0 C2A D:HEM501 4.3 30.5 1.0 C4 D:CPZ503 4.3 38.8 1.0 C3A D:HEM501 4.3 30.5 1.0 C2B D:HEM501 4.3 32.3 1.0 C D:CYS436 4.7 33.4 1.0 N D:LEU437 4.8 33.7 1.0 N D:GLY438 4.8 31.0 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole


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 Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe501 b:39.6 occ:1.00 FE E:HEM501 0.0 39.6 1.0 NA E:HEM501 2.0 38.4 1.0 N1 E:CPZ502 2.0 44.9 1.0 NB E:HEM501 2.0 40.6 1.0 NC E:HEM501 2.0 38.7 1.0 ND E:HEM501 2.2 39.2 1.0 SG E:CYS436 2.4 40.6 1.0 C4A E:HEM501 2.9 38.7 1.0 C1B E:HEM501 3.0 39.0 1.0 C2 E:CPZ502 3.0 46.6 1.0 C5 E:CPZ502 3.0 46.1 1.0 C4C E:HEM501 3.0 40.8 1.0 C1C E:HEM501 3.1 41.9 1.0 C1A E:HEM501 3.1 39.0 1.0 C4B E:HEM501 3.1 41.8 1.0 C1D E:HEM501 3.1 38.0 1.0 C4D E:HEM501 3.2 39.8 1.0 CHB E:HEM501 3.2 40.2 1.0 CB E:CYS436 3.4 42.4 1.0 CHD E:HEM501 3.4 35.8 1.0 CHC E:HEM501 3.5 41.6 1.0 CHA E:HEM501 3.5 39.0 1.0 CA E:CYS436 4.1 39.2 1.0 C3A E:HEM501 4.1 37.9 1.0 N3 E:CPZ502 4.1 45.4 1.0 C4 E:CPZ502 4.2 44.8 1.0 C2B E:HEM501 4.2 41.6 1.0 C3C E:HEM501 4.2 42.1 1.0 C2A E:HEM501 4.2 37.4 1.0 C2C E:HEM501 4.3 42.2 1.0 C3B E:HEM501 4.3 40.4 1.0 C2D E:HEM501 4.4 37.9 1.0 C3D E:HEM501 4.4 35.5 1.0 C E:CYS436 4.9 41.0 1.0 N E:LEU437 4.9 49.5 1.0 N E:GLY438 5.0 42.2 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole


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 Cytochrome P450 2B35 From Desert Woodrat Neotoma Lepida in Complex with 4-(4-Chlorophenyl)Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:46.3 occ:1.00 FE F:HEM501 0.0 46.3 1.0 N1 F:CPZ502 1.9 54.6 1.0 NA F:HEM501 1.9 43.8 1.0 ND F:HEM501 2.0 43.3 1.0 NB F:HEM501 2.0 43.6 1.0 NC F:HEM501 2.1 45.5 1.0 SG F:CYS436 2.7 60.8 1.0 C5 F:CPZ502 2.8 59.6 1.0 C4A F:HEM501 2.9 43.9 1.0 C1B F:HEM501 3.0 45.0 1.0 C4D F:HEM501 3.0 44.4 1.0 C1A F:HEM501 3.0 42.5 1.0 C2 F:CPZ502 3.0 54.9 1.0 C1D F:HEM501 3.0 43.7 1.0 C4C F:HEM501 3.1 45.0 1.0 C4B F:HEM501 3.2 47.6 1.0 C1C F:HEM501 3.2 48.7 1.0 CHB F:HEM501 3.3 43.3 1.0 CHA F:HEM501 3.4 42.5 1.0 CHD F:HEM501 3.4 41.2 1.0 CB F:CYS436 3.4 53.9 1.0 CHC F:HEM501 3.6 48.6 1.0 N3 F:CPZ502 4.0 55.3 1.0 C4 F:CPZ502 4.1 58.2 1.0 CA F:CYS436 4.1 50.4 1.0 C3A F:HEM501 4.2 44.2 1.0 C2A F:HEM501 4.2 42.5 1.0 C3D F:HEM501 4.2 40.1 1.0 C2D F:HEM501 4.2 43.6 1.0 C2B F:HEM501 4.3 45.0 1.0 C3C F:HEM501 4.3 48.9 1.0 C3B F:HEM501 4.4 44.9 1.0 C2C F:HEM501 4.4 48.0 1.0 C F:CYS436 4.9 58.7 1.0 N F:LEU437 4.9 60.2 1.0 N F:GLY438 5.0 53.5 1.0

M.B.Shah, J.Liu, L.Huo, Q.Zhang, M.D.Dearing, P.R.Wilderman, G.D.Szklarz, C.D.Stout, J.R.Halpert. Structure-Function Analysis of Mammalian CYP2B Enzymes Using 7-Substituted Coumarin Derivatives As Probes: Utility of Crystal Structures and Molecular Modeling in Understanding Xenobiotic Metabolism. Mol.Pharmacol. V. 89 435 2016.
ISSN: ESSN 1521-0111
PubMed: 26826176
DOI: 10.1124/MOL.115.102111