Fluorine in PDB 5vwv: Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic

The structure of Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic, PDB code: 5vwv was solved by J.M.Brouwer, P.M.Colman, P.E.Czabotar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.03 / 1.90
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.404, 139.404, 139.404, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 17.7

The structure of Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic (pdb code 5vwv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic, PDB code: 5vwv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:88.8 occ:1.00 F1 A:TFA201 0.0 88.8 1.0 C2 A:TFA201 1.3 81.0 1.0 F3 A:TFA201 2.2 77.2 1.0 F2 A:TFA201 2.2 86.4 1.0 C1 A:TFA201 2.3 53.5 1.0 OXT A:TFA201 2.8 47.2 1.0 O A:TFA201 3.3 52.4 1.0 CD2 B:LEU152 3.3 24.8 1.0 NE A:ARG137 3.5 27.3 1.0 CZ A:PHE93 3.7 35.4 1.0 CE2 A:PHE93 3.8 38.0 1.0 CD A:ARG137 3.9 26.5 1.0 C A:GLY133 4.0 28.9 1.0 N A:PHE134 4.0 24.5 1.0 CE1 A:PHE93 4.2 36.4 1.0 O A:GLY133 4.2 25.2 1.0 CD2 A:PHE93 4.4 34.7 1.0 CA A:GLY133 4.4 21.5 1.0 CA A:PHE134 4.4 22.8 1.0 O A:ALA130 4.5 28.3 1.0 CZ A:ARG137 4.6 28.5 1.0 CG A:ARG137 4.6 24.5 1.0 CD1 A:PHE93 4.7 33.3 1.0 NH2 A:ARG137 4.8 28.0 1.0 CG B:LEU152 4.8 26.5 1.0 O A:HOH313 4.8 50.5 1.0 CG A:PHE93 4.8 30.6 1.0 CD1 B:ILE155 4.9 43.1 1.0 CB A:PHE134 4.9 26.9 1.0

Fluorine binding site 2 out of 3 in the Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:86.4 occ:1.00 F2 A:TFA201 0.0 86.4 1.0 C2 A:TFA201 1.3 81.0 1.0 F1 A:TFA201 2.2 88.8 1.0 F3 A:TFA201 2.2 77.2 1.0 C1 A:TFA201 2.3 53.5 1.0 OXT A:TFA201 2.8 47.2 1.0 O A:TFA201 3.3 52.4 1.0 CD1 B:ILE155 3.3 43.1 1.0 CE2 A:PHE93 3.6 38.0 1.0 CG2 B:ILE155 3.9 43.3 1.0 CD2 A:TYR89 4.0 50.0 1.0 CZ A:PHE93 4.1 35.4 1.0 NE A:ARG137 4.2 27.3 1.0 OD1 A:ASN86 4.3 51.4 1.0 CD2 A:PHE93 4.4 34.7 1.0 CB A:TYR89 4.4 41.1 1.0 NH2 A:ARG137 4.4 28.0 1.0 CG A:TYR89 4.4 39.9 1.0 CG1 B:ILE155 4.5 48.3 1.0 O A:HOH313 4.5 50.5 1.0 CB B:ILE155 4.5 43.6 1.0 CD2 B:LEU152 4.5 24.8 1.0 CE2 A:TYR89 4.7 50.1 1.0 CZ A:ARG137 4.8 28.5 1.0

Fluorine binding site 3 out of 3 in the Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Bak Core Latch Dimer in Complex with Bim-BH3 - Cubic within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:77.2 occ:1.00 F3 A:TFA201 0.0 77.2 1.0 C2 A:TFA201 1.3 81.0 1.0 F1 A:TFA201 2.2 88.8 1.0 F2 A:TFA201 2.2 86.4 1.0 C1 A:TFA201 2.3 53.5 1.0 O A:TFA201 2.6 52.4 1.0 O A:HOH313 2.9 50.5 1.0 OXT A:TFA201 3.5 47.2 1.0 CA A:ALA130 3.8 27.9 1.0 CD2 B:LEU152 3.8 24.8 1.0 O A:ALA130 3.9 28.3 1.0 CB A:ALA130 4.0 26.6 1.0 CG2 B:ILE155 4.2 43.3 1.0 CA A:GLY133 4.2 21.5 1.0 C A:ALA130 4.3 29.7 1.0 O A:HOH432 4.5 60.3 1.0 C A:GLY133 4.5 28.9 1.0 N A:PHE134 4.6 24.5 1.0 OD1 A:ASN86 4.6 51.4 1.0 CD1 B:ILE155 4.7 43.1 1.0 CB B:ILE155 4.9 43.6 1.0 N A:ALA130 4.9 26.9 1.0 N A:GLY133 4.9 20.8 1.0 O A:VAL129 4.9 30.4 1.0

J.M.Brouwer, P.Lan, A.D.Cowan, J.P.Bernardini, R.W.Birkinshaw, M.F.Van Delft, B.E.Sleebs, A.Y.Robin, A.Wardak, I.K.Tan, B.Reljic, E.F.Lee, W.D.Fairlie, M.J.Call, B.J.Smith, G.Dewson, G.Lessene, P.M.Colman, P.E.Czabotar. Conversion of Bim-BH3 From Activator to Inhibitor of Bak Through Structure-Based Design. Mol. Cell V. 68 659 2017.
ISSN: ISSN 1097-4164
PubMed: 29149594
DOI: 10.1016/J.MOLCEL.2017.11.001