Iron in PDB 6dwm: Structure of Human Cytochrome P450 1A1 with Bergamottin

All present enzymatic activity of Structure of Human Cytochrome P450 1A1 with Bergamottin:
1.14.14.1;

The structure of Structure of Human Cytochrome P450 1A1 with Bergamottin, PDB code: 6dwm was solved by A.G.Bart, E.E.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.36 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.330, 194.758, 236.137, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24

The binding sites of Iron atom in the Structure of Human Cytochrome P450 1A1 with Bergamottin (pdb code 6dwm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Human Cytochrome P450 1A1 with Bergamottin, PDB code: 6dwm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Human Cytochrome P450 1A1 with Bergamottin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Human Cytochrome P450 1A1 with Bergamottin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:53.3 occ:1.00 FE A:HEM601 0.0 53.3 1.0 NB A:HEM601 2.0 46.7 1.0 NA A:HEM601 2.0 49.7 1.0 NC A:HEM601 2.1 59.4 1.0 ND A:HEM601 2.1 50.6 1.0 HG A:CYS457 2.3 70.3 1.0 SG A:CYS457 2.7 58.5 1.0 HB2 A:CYS457 2.9 57.0 1.0 C4B A:HEM601 3.0 47.4 1.0 C1B A:HEM601 3.0 42.5 1.0 C1C A:HEM601 3.0 51.8 1.0 C4A A:HEM601 3.1 41.7 1.0 C4C A:HEM601 3.1 55.6 1.0 C1A A:HEM601 3.1 47.2 1.0 C1D A:HEM601 3.1 51.4 1.0 C4D A:HEM601 3.1 49.0 1.0 CB A:CYS457 3.3 47.5 1.0 CHC A:HEM601 3.4 43.5 1.0 CHB A:HEM601 3.4 40.9 1.0 CHD A:HEM601 3.5 46.4 1.0 CHA A:HEM601 3.5 49.3 1.0 HA A:CYS457 3.6 56.2 1.0 CA A:CYS457 4.0 46.8 1.0 HB3 A:CYS457 4.1 57.0 1.0 H A:GLY459 4.1 59.8 1.0 HD1 A:PHE450 4.2 60.0 1.0 C3B A:HEM601 4.2 43.1 1.0 C2C A:HEM601 4.3 47.6 1.0 C2B A:HEM601 4.3 42.4 1.0 C3C A:HEM601 4.3 54.6 1.0 C3A A:HEM601 4.3 41.4 1.0 C2A A:HEM601 4.3 42.2 1.0 C2D A:HEM601 4.3 53.5 1.0 HB1 A:ALA317 4.3 59.7 1.0 C3D A:HEM601 4.3 45.8 1.0 HHC A:HEM601 4.4 52.4 1.0 HG21 A:THR321 4.4 62.1 1.0 HHB A:HEM601 4.4 49.2 1.0 H052 A:HJJ602 4.4 63.1 1.0 HHD A:HEM601 4.4 55.8 1.0 HHA A:HEM601 4.4 59.2 1.0 H A:ILE458 4.5 63.9 1.0 H031 A:HJJ602 4.8 70.8 1.0 C03 A:HJJ602 4.8 58.9 1.0 H252 A:HJJ602 4.9 69.6 1.0 N A:ILE458 4.9 53.1 1.0 C A:CYS457 4.9 55.7 1.0 HE1 A:PHE450 4.9 58.9 1.0 N A:GLY459 5.0 49.7 1.0

Iron binding site 2 out of 4 in the Structure of Human Cytochrome P450 1A1 with Bergamottin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Human Cytochrome P450 1A1 with Bergamottin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:46.4 occ:1.00 FE B:HEM601 0.0 46.4 1.0 NB B:HEM601 2.0 45.9 1.0 NC B:HEM601 2.1 43.1 1.0 ND B:HEM601 2.1 44.1 1.0 NA B:HEM601 2.1 52.1 1.0 SG B:CYS457 2.6 44.8 1.0 HB2 B:CYS457 3.0 50.8 1.0 C1B B:HEM601 3.0 44.9 1.0 C4B B:HEM601 3.0 46.8 1.0 C1C B:HEM601 3.1 42.9 1.0 C4A B:HEM601 3.1 40.6 1.0 C4C B:HEM601 3.1 41.6 1.0 C1D B:HEM601 3.1 42.6 1.0 C4D B:HEM601 3.1 44.1 1.0 H013 B:HJJ602 3.1 82.3 1.0 C1A B:HEM601 3.1 44.8 1.0 CB B:CYS457 3.3 42.2 1.0 CHB B:HEM601 3.4 37.6 1.0 CHC B:HEM601 3.4 46.1 1.0 CHD B:HEM601 3.4 38.8 1.0 CHA B:HEM601 3.5 50.2 1.0 HA B:CYS457 3.6 51.5 1.0 C01 B:HJJ602 4.0 68.5 1.0 CA B:CYS457 4.0 42.8 1.0 H042 B:HJJ602 4.1 69.2 1.0 HB3 B:CYS457 4.1 50.8 1.0 H011 B:HJJ602 4.1 82.3 1.0 H B:GLY459 4.1 51.9 1.0 C2B B:HEM601 4.2 40.0 1.0 HB1 B:ALA317 4.2 51.3 1.0 C3B B:HEM601 4.2 40.4 1.0 C2C B:HEM601 4.3 45.0 1.0 C3C B:HEM601 4.3 45.9 1.0 C2D B:HEM601 4.3 46.4 1.0 C3D B:HEM601 4.3 42.3 1.0 C3A B:HEM601 4.3 44.9 1.0 C2A B:HEM601 4.3 45.2 1.0 HG21 B:THR321 4.3 72.8 1.0 HHB B:HEM601 4.4 45.2 1.0 HHC B:HEM601 4.4 55.4 1.0 H B:ILE458 4.4 53.6 1.0 HD1 B:PHE450 4.4 59.7 1.0 HHD B:HEM601 4.4 46.7 1.0 HHA B:HEM601 4.4 60.4 1.0 H012 B:HJJ602 4.6 82.3 1.0 C02 B:HJJ602 4.7 52.2 1.0 HG1 B:THR321 4.8 68.3 1.0 N B:ILE458 4.8 44.6 1.0 C B:CYS457 4.9 47.4 1.0 C04 B:HJJ602 4.9 57.6 1.0 N B:GLY459 5.0 43.1 1.0

Iron binding site 3 out of 4 in the Structure of Human Cytochrome P450 1A1 with Bergamottin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Human Cytochrome P450 1A1 with Bergamottin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:65.1 occ:1.00 FE C:HEM601 0.0 65.1 1.0 ND C:HEM601 2.0 62.2 1.0 NC C:HEM601 2.0 62.4 1.0 NB C:HEM601 2.1 56.1 1.0 NA C:HEM601 2.1 59.6 1.0 SG C:CYS457 2.9 74.0 1.0 C4D C:HEM601 3.0 65.4 1.0 C1C C:HEM601 3.0 61.3 1.0 C4B C:HEM601 3.0 59.3 1.0 C1D C:HEM601 3.1 58.1 1.0 C1A C:HEM601 3.1 61.7 1.0 C4C C:HEM601 3.1 63.8 1.0 C4A C:HEM601 3.1 61.5 1.0 C1B C:HEM601 3.1 58.4 1.0 HB2 C:CYS457 3.1 94.8 1.0 CHC C:HEM601 3.4 59.5 1.0 CHA C:HEM601 3.4 65.9 1.0 CHD C:HEM601 3.4 59.8 1.0 CB C:CYS457 3.5 78.9 1.0 CHB C:HEM601 3.5 63.5 1.0 HA C:CYS457 3.6 91.8 1.0 HB1 C:ALA317 4.1 86.0 1.0 CA C:CYS457 4.1 76.4 1.0 H C:GLY459 4.2 90.5 1.0 C2D C:HEM601 4.3 63.5 1.0 C3D C:HEM601 4.3 65.8 1.0 C2C C:HEM601 4.3 58.9 1.0 C3C C:HEM601 4.3 59.4 1.0 C3B C:HEM601 4.3 61.6 1.0 C2A C:HEM601 4.3 69.2 1.0 H041 C:HJJ602 4.3 85.0 1.0 C2B C:HEM601 4.3 59.8 1.0 C3A C:HEM601 4.3 64.7 1.0 HB3 C:CYS457 4.3 94.8 1.0 H C:ILE458 4.4 86.9 1.0 HHC C:HEM601 4.4 71.5 1.0 HHA C:HEM601 4.4 79.2 1.0 HHD C:HEM601 4.4 71.9 1.0 HG21 C:THR321 4.4 78.6 1.0 HHB C:HEM601 4.4 76.3 1.0 H031 C:HJJ602 4.6 86.1 1.0 HD1 C:PHE450 4.6 81.7 1.0 C03 C:HJJ602 4.7 71.7 1.0 N C:ILE458 4.9 72.3 1.0 C04 C:HJJ602 4.9 70.8 1.0 C C:CYS457 4.9 78.9 1.0 CB C:ALA317 5.0 71.6 1.0

Iron binding site 4 out of 4 in the Structure of Human Cytochrome P450 1A1 with Bergamottin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Human Cytochrome P450 1A1 with Bergamottin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:60.7 occ:1.00 FE D:HEM601 0.0 60.7 1.0 ND D:HEM601 2.0 56.4 1.0 NC D:HEM601 2.0 53.9 1.0 NA D:HEM601 2.1 52.9 1.0 NB D:HEM601 2.1 55.6 1.0 HG D:CYS457 2.3 89.5 1.0 SG D:CYS457 2.7 74.5 1.0 HB2 D:CYS457 3.0 71.9 1.0 C4D D:HEM601 3.0 60.8 1.0 C1D D:HEM601 3.0 61.0 1.0 C1C D:HEM601 3.0 57.5 1.0 C4C D:HEM601 3.0 53.4 1.0 C4B D:HEM601 3.1 55.3 1.0 C1A D:HEM601 3.1 55.0 1.0 C4A D:HEM601 3.1 55.2 1.0 C1B D:HEM601 3.1 53.9 1.0 CB D:CYS457 3.4 59.8 1.0 CHA D:HEM601 3.4 61.0 1.0 CHD D:HEM601 3.4 57.2 1.0 CHC D:HEM601 3.4 55.1 1.0 CHB D:HEM601 3.5 54.3 1.0 HA D:CYS457 3.7 73.6 1.0 HB1 D:ALA317 4.0 82.8 1.0 CA D:CYS457 4.1 61.2 1.0 H D:GLY459 4.2 73.9 1.0 HB3 D:CYS457 4.2 71.9 1.0 C2C D:HEM601 4.2 55.5 1.0 C3C D:HEM601 4.2 56.1 1.0 C2D D:HEM601 4.3 62.0 1.0 C3D D:HEM601 4.3 62.5 1.0 H041 D:HJJ602 4.3 81.5 1.0 C3B D:HEM601 4.3 50.1 1.0 C2A D:HEM601 4.3 61.8 1.0 C3A D:HEM601 4.3 57.9 1.0 C2B D:HEM601 4.3 53.9 1.0 HD1 D:PHE450 4.4 64.3 1.0 HHA D:HEM601 4.4 73.3 1.0 HHD D:HEM601 4.4 68.8 1.0 HHC D:HEM601 4.4 66.3 1.0 HG21 D:THR321 4.4 81.1 1.0 HHB D:HEM601 4.4 65.3 1.0 H D:ILE458 4.5 72.1 1.0 C03 D:HJJ602 4.7 75.2 1.0 H031 D:HJJ602 4.7 90.3 1.0 H253 D:HJJ602 4.9 79.7 1.0 CB D:ALA317 4.9 69.0 1.0 N D:ILE458 4.9 60.0 1.0 C04 D:HJJ602 4.9 67.8 1.0 C02 D:HJJ602 5.0 66.1 1.0 C D:CYS457 5.0 62.7 1.0 H011 D:HJJ602 5.0 78.0 1.0

A.G.Bart, E.E.Scott. Structures of Human Cytochrome P450 1A1 with Bergamottin and Erlotinib Reveal Active-Site Modifications For Binding of Diverse Ligands. J. Biol. Chem. V. 293 19201 2018.
ISSN: ESSN 1083-351X
PubMed: 30254074
DOI: 10.1074/JBC.RA118.005588