Bromine in PDB 5uap: Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide

The structure of Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide, PDB code: 5uap 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)	50.59 / 2.03
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	77.070, 77.070, 202.172, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 20.6

The structure of Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Bromine atom in the Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide (pdb code 5uap). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide, PDB code: 5uap:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br505 b:63.8 occ:0.35 BR1 A:82S505 0.0 63.8 0.3 C8 A:82S505 1.7 40.6 0.7 C2 A:82S505 2.0 58.3 0.3 C9 A:82S505 2.8 57.0 0.3 O A:HOH872 2.8 44.3 1.0 C1 A:82S505 2.9 57.4 0.3 C7 A:82S505 2.9 42.1 0.7 C3 A:82S505 2.9 57.3 0.3 C10 A:82S505 3.1 52.4 0.3 C10 A:82S505 3.1 42.9 0.7 C1 A:82S505 3.3 41.9 0.7 C7 A:82S505 3.4 58.9 0.3 C9 A:82S505 3.5 39.0 0.7 CD1 A:ILE114 3.6 21.0 1.0 C6 A:82S505 3.7 42.7 0.7 CB A:ALA298 3.8 23.4 1.0 C4 A:82S505 3.9 59.0 0.3 C4D A:HEM501 4.1 17.8 1.0 CG2 A:ILE114 4.1 21.5 1.0 C4 A:82S505 4.1 42.0 0.7 C5 A:82S505 4.2 42.4 0.7 CHA A:HEM501 4.2 19.1 1.0 C6 A:82S505 4.2 58.2 0.3 CG1 A:ILE114 4.3 18.7 1.0 ND A:HEM501 4.4 19.0 1.0 C3D A:HEM501 4.4 19.4 1.0 C1A A:HEM501 4.5 16.6 1.0 CG2 A:VAL367 4.5 17.2 1.0 CA A:ALA298 4.6 25.9 1.0 C8 A:82S505 4.7 60.7 0.3 C5 A:82S505 4.7 60.0 0.3 C1D A:HEM501 4.8 17.1 1.0 C2 A:82S505 4.8 44.4 0.7 NA A:HEM501 4.8 17.2 1.0 CB A:ILE114 4.8 20.5 1.0 C2D A:HEM501 4.8 18.6 1.0 CAD A:HEM501 5.0 19.0 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br505 b:38.4 occ:0.65 BR1 A:82S505 0.0 38.4 0.7 C2 A:82S505 2.0 44.4 0.7 C8 A:82S505 2.2 60.7 0.3 C9 A:82S505 2.8 39.0 0.7 C1 A:82S505 2.9 41.9 0.7 C3 A:82S505 2.9 39.4 0.7 C10 A:82S505 3.0 52.4 0.3 C10 A:82S505 3.1 42.9 0.7 C7 A:82S505 3.2 58.9 0.3 C7 A:82S505 3.4 42.1 0.7 C1 A:82S505 3.5 57.4 0.3 C9 A:82S505 3.7 57.0 0.3 CE2 A:PHE297 3.7 34.4 1.0 CD2 A:PHE297 3.8 33.9 1.0 C4 A:82S505 3.9 42.0 0.7 C6 A:82S505 4.0 58.2 0.3 CE2 A:PHE115 4.1 19.7 1.0 CZ A:PHE115 4.1 19.1 1.0 C6 A:82S505 4.2 42.7 0.7 CG2 A:VAL104 4.3 23.1 1.0 CE2 A:PHE108 4.4 22.7 1.0 CG1 A:VAL104 4.4 21.6 1.0 CZ A:PHE297 4.5 32.9 1.0 CG A:PHE297 4.5 30.2 1.0 C4 A:82S505 4.5 59.0 0.3 CD1 A:ILE209 4.6 21.6 1.0 C5 A:82S505 4.6 60.0 0.3 C8 A:82S505 4.7 40.6 0.7 C5 A:82S505 4.7 42.4 0.7 CZ A:PHE108 4.8 20.2 1.0 CB A:VAL104 4.8 22.4 1.0 C2 A:82S505 4.9 58.3 0.3

Bromine binding site 3 out of 4 in the Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide within 5.0Å range: probe atom residue distance (Å) B Occ B:Br505 b:60.2 occ:0.35 BR1 B:82S505 0.0 60.2 0.3 C8 B:82S505 1.6 37.2 0.7 C2 B:82S505 2.0 52.0 0.3 C7 B:82S505 2.7 39.9 0.7 C9 B:82S505 2.8 50.7 0.3 C1 B:82S505 2.9 51.7 0.3 C3 B:82S505 2.9 49.7 0.3 C10 B:82S505 3.0 41.4 0.7 O B:HOH839 3.0 46.0 1.0 C10 B:82S505 3.1 50.0 0.3 C1 B:82S505 3.2 40.6 0.7 C7 B:82S505 3.4 51.7 0.3 C9 B:82S505 3.4 37.1 0.7 C6 B:82S505 3.6 42.3 0.7 CD1 B:ILE114 3.6 21.7 1.0 CB B:ALA298 3.8 24.6 1.0 C4 B:82S505 3.9 50.7 0.3 C4 B:82S505 4.0 41.5 0.7 C5 B:82S505 4.1 41.3 0.7 CG2 B:ILE114 4.1 23.0 1.0 C4D B:HEM501 4.2 17.0 1.0 C6 B:82S505 4.2 50.3 0.3 CHA B:HEM501 4.3 19.0 1.0 CG1 B:ILE114 4.3 21.8 1.0 CG2 B:VAL367 4.6 17.7 1.0 CA B:ALA298 4.6 26.3 1.0 C3D B:HEM501 4.6 19.1 1.0 ND B:HEM501 4.6 17.8 1.0 C1A B:HEM501 4.6 16.4 1.0 C2 B:82S505 4.6 42.7 0.7 C8 B:82S505 4.7 51.2 0.3 C5 B:82S505 4.7 49.2 0.3 CB B:ILE114 4.9 22.1 1.0 NA B:HEM501 4.9 15.9 1.0 C1D B:HEM501 4.9 17.1 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of CYP2B6 (Y226H/K262R) in Complex with Bornyl Bromide within 5.0Å range: probe atom residue distance (Å) B Occ B:Br505 b:37.5 occ:0.65 BR1 B:82S505 0.0 37.5 0.7 C2 B:82S505 2.0 42.7 0.7 C8 B:82S505 2.4 51.2 0.3 C9 B:82S505 2.8 37.1 0.7 C10 B:82S505 2.8 50.0 0.3 C1 B:82S505 2.9 40.6 0.7 C3 B:82S505 2.9 40.0 0.7 C10 B:82S505 3.1 41.4 0.7 C7 B:82S505 3.2 51.7 0.3 C7 B:82S505 3.4 39.9 0.7 C1 B:82S505 3.5 51.7 0.3 CE2 B:PHE297 3.7 34.6 1.0 C9 B:82S505 3.7 50.7 0.3 CD2 B:PHE297 3.7 33.4 1.0 C4 B:82S505 3.9 41.5 0.7 C6 B:82S505 4.0 50.3 0.3 CE2 B:PHE115 4.1 19.1 1.0 CZ B:PHE115 4.1 18.0 1.0 C6 B:82S505 4.3 42.3 0.7 CG2 B:VAL104 4.3 21.9 1.0 CE2 B:PHE108 4.4 21.9 1.0 CZ B:PHE297 4.4 35.0 1.0 CG1 B:VAL104 4.4 21.3 1.0 CG B:PHE297 4.5 32.1 1.0 CD1 B:ILE209 4.6 21.9 1.0 C4 B:82S505 4.6 50.7 0.3 C5 B:82S505 4.7 49.2 0.3 C8 B:82S505 4.7 37.2 0.7 C5 B:82S505 4.7 41.3 0.7 CZ B:PHE108 4.8 18.7 1.0 CB B:VAL104 4.8 21.3 1.0 C2 B:82S505 4.9 52.0 0.3

M.B.Shah, J.Liu, Q.Zhang, C.D.Stout, J.R.Halpert. Halogen-Pi Interactions in the Cytochrome P450 Active Site: Structural Insights Into Human CYP2B6 Substrate Selectivity. Acs Chem. Biol. V. 12 1204 2017.
ISSN: ESSN 1554-8937
PubMed: 28368100
DOI: 10.1021/ACSCHEMBIO.7B00056