Bromine in PDB 5ufg: Crystal Structure of CYP2B6 (Y226H/K262R/I114V) in Complex with Myrtenyl Bromide

The structure of Crystal Structure of CYP2B6 (Y226H/K262R/I114V) in Complex with Myrtenyl Bromide, PDB code: 5ufg 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)	40.40 / 1.76
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.120, 77.120, 202.201, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 20.4

The structure of Crystal Structure of CYP2B6 (Y226H/K262R/I114V) in Complex with Myrtenyl Bromide also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Bromine atom in the Crystal Structure of CYP2B6 (Y226H/K262R/I114V) in Complex with Myrtenyl Bromide (pdb code 5ufg). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Crystal Structure of CYP2B6 (Y226H/K262R/I114V) in Complex with Myrtenyl Bromide, PDB code: 5ufg:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Crystal Structure of CYP2B6 (Y226H/K262R/I114V) in Complex with Myrtenyl 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/I114V) in Complex with Myrtenyl Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br505 b:39.9 occ:0.40 BR1 A:85D505 0.0 39.9 0.4 C6 A:85D505 0.9 12.1 0.4 C9 A:85D505 1.3 9.4 0.4 C8 A:85D505 1.5 32.6 0.4 C1 A:85D505 1.9 27.4 0.4 C10 A:85D505 1.9 24.1 0.4 C7 A:85D505 2.1 14.4 0.2 C5 A:85D505 2.4 27.0 0.4 C5 A:85D505 2.7 16.0 0.2 C2 A:85D505 2.7 20.7 0.4 C2 A:85D505 2.8 34.8 0.4 C7 A:85D505 2.8 18.3 0.4 C3 A:85D505 3.0 39.9 0.4 C4 A:85D505 3.3 61.0 0.4 C3 A:85D505 3.4 16.3 0.4 C4 A:85D505 3.5 25.0 0.2 C1 A:85D505 3.6 13.7 0.2 C10 A:85D505 3.7 14.6 0.4 BR1 A:85D505 3.8 23.4 0.4 C6 A:85D505 3.9 3.1 0.2 CE2 A:PHE297 3.9 36.2 1.0 C1 A:85D505 4.0 37.6 0.4 C8 A:85D505 4.0 41.8 0.4 CD1 A:ILE209 4.1 23.2 1.0 CG2 A:VAL104 4.1 17.5 1.0 CZ A:PHE115 4.1 23.9 1.0 CD2 A:PHE297 4.1 32.0 1.0 C3 A:85D505 4.2 13.8 0.2 CG1 A:VAL104 4.2 18.1 1.0 C2 A:85D505 4.3 6.9 0.2 C9 A:85D505 4.3 7.7 0.2 C4 A:85D505 4.3 32.9 0.4 CE2 A:PHE115 4.5 25.7 1.0 C6 A:85D505 4.6 25.2 0.4 CZ A:PHE297 4.6 32.0 1.0 CD1 A:ILE101 4.6 18.4 1.0 CB A:VAL104 4.7 19.4 1.0

Bromine binding site 2 out of 3 in the Crystal Structure of CYP2B6 (Y226H/K262R/I114V) in Complex with Myrtenyl 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/I114V) in Complex with Myrtenyl Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br505 b:23.4 occ:0.40 BR1 A:85D505 0.0 23.4 0.4 C10 A:85D505 1.9 14.6 0.4 C3 A:85D505 2.6 39.9 0.4 C2 A:85D505 2.7 34.8 0.4 C1 A:85D505 2.8 27.4 0.4 C7 A:85D505 3.1 14.4 0.2 C4 A:85D505 3.3 32.9 0.4 C1 A:85D505 3.4 13.7 0.2 C2 A:85D505 3.5 20.7 0.4 CB A:PHE297 3.8 24.2 1.0 C10 A:85D505 3.8 24.1 0.4 BR1 A:85D505 3.8 39.9 0.4 CD2 A:PHE297 3.9 32.0 1.0 CE2 A:PHE115 3.9 25.7 1.0 O A:SER294 4.0 23.2 1.0 CA A:SER294 4.0 18.9 1.0 C6 A:85D505 4.0 12.1 0.4 C3 A:85D505 4.1 16.3 0.4 C2 A:85D505 4.1 6.9 0.2 C7 A:85D505 4.1 18.3 0.4 CG A:PHE297 4.1 28.7 1.0 OG A:SER294 4.2 22.3 1.0 CG1 A:VAL114 4.2 18.5 1.0 CG2 A:VAL114 4.3 17.6 1.0 C8 A:85D505 4.3 32.6 0.4 CZ A:PHE108 4.4 21.8 1.0 C10 A:85D505 4.4 2.0 0.2 CB A:SER294 4.4 15.5 1.0 CB A:VAL114 4.5 16.9 1.0 N A:ALA298 4.5 25.9 1.0 CZ A:PHE115 4.5 23.9 1.0 C A:SER294 4.5 19.9 1.0 C5 A:85D505 4.6 22.2 0.4 C6 A:85D505 4.6 3.1 0.2 C5 A:85D505 4.6 16.0 0.2 C7 A:85D505 4.6 15.6 0.4 C1 A:85D505 4.7 37.6 0.4 CE2 A:PHE108 4.7 22.8 1.0 C9 A:85D505 4.7 9.4 0.4 C9 A:85D505 4.8 7.7 0.2 CB A:ALA298 4.8 25.4 1.0 CE2 A:PHE297 4.8 36.2 1.0 CD2 A:PHE115 4.9 25.2 1.0 C5 A:85D505 4.9 27.0 0.4 CE1 A:PHE108 4.9 19.3 1.0 CA A:PHE297 4.9 24.5 1.0 C A:PHE297 4.9 25.5 1.0

Bromine binding site 3 out of 3 in the Crystal Structure of CYP2B6 (Y226H/K262R/I114V) in Complex with Myrtenyl 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/I114V) in Complex with Myrtenyl Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br505 b:43.5 occ:0.20 BR1 A:85D505 0.0 43.5 0.2 C7 A:85D505 1.9 15.6 0.4 C10 A:85D505 1.9 2.0 0.2 O A:HOH804 2.1 47.3 1.0 C5 A:85D505 2.3 22.2 0.4 C2 A:85D505 2.7 6.9 0.2 C6 A:85D505 3.3 25.2 0.4 C1 A:85D505 3.4 37.6 0.4 NA A:HEM501 3.4 15.9 1.0 C1A A:HEM501 3.4 18.9 1.0 C1 A:85D505 3.4 13.7 0.2 C9 A:85D505 3.5 47.6 0.4 ND A:HEM501 3.5 18.4 1.0 C8 A:85D505 3.5 12.0 0.2 C4 A:85D505 3.5 32.9 0.4 C4D A:HEM501 3.5 18.2 1.0 CHA A:HEM501 3.5 20.6 1.0 C3 A:85D505 3.6 13.8 0.2 CB A:ALA298 3.6 25.4 1.0 FE A:HEM501 3.8 16.0 1.0 C6 A:85D505 4.0 3.1 0.2 C4A A:HEM501 4.2 15.8 1.0 C2 A:85D505 4.2 20.7 0.4 C3 A:85D505 4.3 16.3 0.4 C3 A:85D505 4.3 39.9 0.4 C2A A:HEM501 4.3 13.4 1.0 C1D A:HEM501 4.3 18.0 1.0 CA A:ALA298 4.3 28.0 1.0 CD1 A:LEU363 4.4 15.8 1.0 CG2 A:THR302 4.4 21.4 1.0 C3D A:HEM501 4.4 17.1 1.0 C2 A:85D505 4.5 34.8 0.4 NB A:HEM501 4.6 17.4 1.0 C10 A:85D505 4.6 14.6 0.4 C3A A:HEM501 4.6 17.1 1.0 C7 A:85D505 4.7 18.3 0.4 CG2 A:VAL367 4.7 16.5 1.0 O A:ALA298 4.7 34.8 1.0 C8 A:85D505 4.7 41.8 0.4 C4 A:85D505 4.7 25.0 0.2 C4 A:85D505 4.8 61.0 0.4 NC A:HEM501 4.8 16.3 1.0 CHB A:HEM501 4.9 15.3 1.0 C2D A:HEM501 4.9 19.2 1.0 C7 A:85D505 4.9 14.4 0.2 C5 A:85D505 5.0 16.0 0.2

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