Chlorine 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
Iron	(Fe)	6 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502 b:0.3 occ:1.00 CL A:9ZJ502 0.0 0.3 1.0 CAO A:9ZJ502 1.7 0.2 1.0 CAJ A:9ZJ502 2.7 0.4 1.0 CAH A:9ZJ502 2.7 0.3 1.0 CE2 A:PHE108 3.4 23.9 1.0 CZ A:PHE108 3.6 23.9 1.0 CAQ A:9ZJ502 4.0 1.0 1.0 CAI A:9ZJ502 4.0 0.7 1.0 CE1 A:PHE115 4.3 46.2 1.0 FAC A:9ZJ502 4.3 0.4 1.0 CD2 A:PHE297 4.4 48.0 1.0 CD2 A:PHE108 4.5 25.3 1.0 CAP A:9ZJ502 4.5 0.0 1.0 CE2 A:PHE297 4.6 46.8 1.0 CG1 A:VAL104 4.6 34.8 1.0 CG A:PHE297 4.6 41.3 1.0 CG2 A:VAL104 4.6 32.7 1.0 CE1 A:PHE108 4.7 25.5 1.0 CD2 A:LEU238 4.7 37.5 1.0 CZ A:PHE115 4.7 47.4 1.0 CB A:VAL104 4.8 38.2 1.0 CD1 A:LEU293 4.8 36.1 1.0 CZ A:PHE297 5.0 47.6 1.0 CD1 A:PHE297 5.0 41.8 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502 b:94.2 occ:1.00 CL B:9ZJ502 0.0 94.2 1.0 CAO B:9ZJ502 1.7 0.8 1.0 CAH B:9ZJ502 2.7 0.2 1.0 CAJ B:9ZJ502 2.7 99.1 1.0 CE2 B:PHE108 3.4 32.4 1.0 CZ B:PHE108 3.5 22.1 1.0 CAQ B:9ZJ502 4.0 0.2 1.0 CAI B:9ZJ502 4.0 0.3 1.0 FAC B:9ZJ502 4.3 0.1 1.0 CE1 B:PHE115 4.3 36.8 1.0 CD2 B:PHE108 4.5 41.2 1.0 CD2 B:PHE297 4.5 53.9 1.0 CAP B:9ZJ502 4.5 0.6 1.0 CG1 B:VAL104 4.5 33.7 1.0 CE1 B:PHE108 4.6 29.7 1.0 CG B:PHE297 4.6 45.3 1.0 CG2 B:VAL104 4.6 32.3 1.0 CE2 B:PHE297 4.7 58.9 1.0 CD2 B:LEU238 4.7 26.7 1.0 CZ B:PHE115 4.8 44.5 1.0 CB B:VAL104 4.8 32.7 1.0 CD1 B:PHE297 5.0 47.2 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502 b:88.7 occ:1.00 CL C:9ZJ502 0.0 88.7 1.0 CAO C:9ZJ502 1.7 94.3 1.0 CAJ C:9ZJ502 2.7 91.5 1.0 CAH C:9ZJ502 2.7 98.2 1.0 CE2 C:PHE108 3.3 34.3 1.0 CZ C:PHE108 3.5 32.1 1.0 CAQ C:9ZJ502 4.0 88.9 1.0 CAI C:9ZJ502 4.0 99.7 1.0 CE1 C:PHE115 4.3 43.1 1.0 FAC C:9ZJ502 4.3 84.8 1.0 CD2 C:PHE108 4.5 35.0 1.0 CAP C:9ZJ502 4.5 92.4 1.0 CG1 C:VAL104 4.6 33.9 1.0 CD2 C:LEU238 4.6 22.5 1.0 CG2 C:VAL104 4.6 23.6 1.0 CE1 C:PHE108 4.7 37.6 1.0 CD2 C:PHE297 4.7 26.7 1.0 CB C:VAL104 4.8 30.8 1.0 CZ C:PHE115 4.9 45.4 1.0 CG C:PHE297 4.9 28.3 1.0 CE2 C:PHE297 4.9 38.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502 b:0.5 occ:1.00 CL D:9ZJ502 0.0 0.5 1.0 CAO D:9ZJ502 1.7 0.5 1.0 CAH D:9ZJ502 2.7 0.7 1.0 CAJ D:9ZJ502 2.7 0.3 1.0 CE2 D:PHE108 3.3 46.3 1.0 CZ D:PHE108 3.4 43.7 1.0 CAQ D:9ZJ502 4.0 98.0 1.0 CAI D:9ZJ502 4.0 0.2 1.0 CE1 D:PHE115 4.2 46.4 1.0 FAC D:9ZJ502 4.3 79.3 1.0 CD2 D:PHE108 4.4 47.4 1.0 CD2 D:PHE297 4.5 58.6 1.0 CAP D:9ZJ502 4.5 0.3 1.0 CG1 D:VAL104 4.6 41.0 1.0 CG D:PHE297 4.6 49.4 1.0 CE1 D:PHE108 4.6 46.0 1.0 CE2 D:PHE297 4.6 58.1 1.0 CG2 D:VAL104 4.6 43.2 1.0 CD2 D:LEU238 4.7 46.9 1.0 CB D:VAL104 4.8 41.7 1.0 CD1 D:LEU293 4.8 42.7 1.0 CZ D:PHE115 4.9 48.4 1.0 CD1 D:PHE297 4.9 51.1 1.0 CZ D:PHE297 5.0 45.8 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502 b:96.1 occ:1.00 CL E:9ZJ502 0.0 96.1 1.0 CAO E:9ZJ502 1.7 0.8 1.0 CAJ E:9ZJ502 2.7 95.6 1.0 CAH E:9ZJ502 2.7 0.1 1.0 CE2 E:PHE108 3.3 38.0 1.0 CZ E:PHE108 3.5 44.6 1.0 CAQ E:9ZJ502 4.0 96.0 1.0 CAI E:9ZJ502 4.0 0.1 1.0 CE1 E:PHE115 4.2 41.0 1.0 FAC E:9ZJ502 4.3 87.8 1.0 CD2 E:PHE297 4.4 57.4 1.0 CD2 E:PHE108 4.4 39.2 1.0 CAP E:9ZJ502 4.5 0.4 1.0 CG1 E:VAL104 4.5 42.8 1.0 CE2 E:PHE297 4.6 63.4 1.0 CG E:PHE297 4.6 47.9 1.0 CD2 E:LEU238 4.6 23.8 1.0 CE1 E:PHE108 4.7 38.4 1.0 CG2 E:VAL104 4.7 42.6 1.0 CB E:VAL104 4.8 42.0 1.0 CZ E:PHE115 4.8 36.5 1.0 CD1 E:LEU293 4.9 17.6 1.0 CD1 E:PHE297 4.9 52.0 1.0 CZ E:PHE297 4.9 56.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl503 b:87.6 occ:1.00 CL F:9ZJ503 0.0 87.6 1.0 CAO F:9ZJ503 1.7 91.2 1.0 CAH F:9ZJ503 2.7 96.5 1.0 CAJ F:9ZJ503 2.7 86.5 1.0 CE2 F:PHE108 3.5 35.7 1.0 CZ F:PHE108 3.5 26.8 1.0 CAQ F:9ZJ503 4.0 87.1 1.0 CAI F:9ZJ503 4.0 98.8 1.0 CE1 F:PHE115 4.2 48.4 1.0 FAC F:9ZJ503 4.3 85.9 1.0 CD2 F:PHE297 4.5 60.6 1.0 CAP F:9ZJ503 4.5 95.0 1.0 CD2 F:PHE108 4.6 39.0 1.0 CE1 F:PHE108 4.6 34.7 1.0 CG1 F:VAL104 4.6 40.9 1.0 CG2 F:VAL104 4.6 30.4 1.0 CG F:PHE297 4.6 52.2 1.0 CE2 F:PHE297 4.6 66.3 1.0 CD2 F:LEU238 4.7 23.3 1.0 CB F:VAL104 4.8 37.9 1.0 CZ F:PHE115 4.8 43.4 1.0 CD1 F:PHE297 5.0 53.5 1.0 CD1 F:LEU293 5.0 30.7 1.0 CZ F:PHE297 5.0 68.2 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