Fluorine in PDB 6djz: Human Sigma-1 Receptor Bound to Haloperidol

The structure of Human Sigma-1 Receptor Bound to Haloperidol, PDB code: 6djz was solved by H.R.Schmidt, A.C.Kruse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.51 / 3.08
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.556, 126.062, 109.702, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 27.6

The structure of Human Sigma-1 Receptor Bound to Haloperidol also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Fluorine atom in the Human Sigma-1 Receptor Bound to Haloperidol (pdb code 6djz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Sigma-1 Receptor Bound to Haloperidol, PDB code: 6djz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Human Sigma-1 Receptor Bound to Haloperidol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Sigma-1 Receptor Bound to Haloperidol within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:0.7 occ:1.00 F26 A:GMJ301 0.0 0.7 1.0 C03 A:GMJ301 1.4 0.9 1.0 C04 A:GMJ301 2.4 0.6 1.0 C02 A:GMJ301 2.4 0.0 1.0 CD2 A:LEU182 3.5 95.7 1.0 C05 A:GMJ301 3.6 0.6 1.0 CD1 A:TYR206 3.7 95.7 1.0 C01 A:GMJ301 3.7 0.2 1.0 CG A:TYR206 3.9 94.8 1.0 CE1 A:TYR206 4.0 96.4 1.0 C06 A:GMJ301 4.1 0.6 1.0 CG2 A:ILE178 4.2 0.7 1.0 CG A:LEU182 4.2 0.9 1.0 CB A:TYR206 4.3 97.0 1.0 CD2 A:TYR206 4.5 0.6 1.0 CZ A:TYR206 4.6 99.7 1.0 CD1 A:LEU182 4.7 0.7 1.0 CE2 A:TYR206 4.8 95.0 1.0 OG1 A:THR181 5.0 0.4 1.0

Fluorine binding site 2 out of 3 in the Human Sigma-1 Receptor Bound to Haloperidol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Sigma-1 Receptor Bound to Haloperidol within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:0.3 occ:1.00 F26 B:GMJ301 0.0 0.3 1.0 C03 B:GMJ301 1.4 0.2 1.0 C02 B:GMJ301 2.4 0.5 1.0 C04 B:GMJ301 2.4 0.1 1.0 C01 B:GMJ301 3.6 0.9 1.0 C05 B:GMJ301 3.6 0.2 1.0 CG B:TYR206 4.1 0.2 1.0 C06 B:GMJ301 4.1 0.8 1.0 CD1 B:TYR206 4.1 0.5 1.0 CG2 B:ILE178 4.2 0.8 1.0 O B:HOH402 4.2 0.4 1.0 CD2 B:TYR206 4.3 0.1 1.0 CD1 B:LEU182 4.3 0.1 1.0 CE1 B:TYR206 4.4 0.8 1.0 CD2 B:LEU95 4.5 0.6 1.0 CE2 B:TYR206 4.6 0.2 1.0 CB B:TYR206 4.6 0.4 1.0 CZ B:TYR206 4.6 0.5 1.0 CB B:LEU182 4.7 0.8 1.0 CD1 B:LEU95 4.9 94.2 1.0 CG B:LEU182 4.9 0.8 1.0

Fluorine binding site 3 out of 3 in the Human Sigma-1 Receptor Bound to Haloperidol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Sigma-1 Receptor Bound to Haloperidol within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:0.8 occ:1.00 F26 C:GMJ301 0.0 0.8 1.0 C03 C:GMJ301 1.4 0.1 1.0 C02 C:GMJ301 2.4 0.3 1.0 C04 C:GMJ301 2.4 0.9 1.0 CD2 C:LEU95 3.1 81.5 1.0 CD1 C:LEU95 3.3 70.3 1.0 CD1 C:TYR206 3.5 78.9 1.0 C01 C:GMJ301 3.6 0.8 1.0 C05 C:GMJ301 3.6 0.1 1.0 CG C:LEU95 3.8 70.0 1.0 CB C:TYR206 3.8 68.7 1.0 CG C:TYR206 3.9 68.8 1.0 CB C:ALA98 3.9 89.3 1.0 CA C:TYR206 3.9 70.2 1.0 C06 C:GMJ301 4.1 0.4 1.0 N C:TYR206 4.3 80.4 1.0 CE1 C:TYR206 4.3 83.1 1.0 CB C:LEU95 4.5 76.2 1.0 C C:SER205 4.9 81.1 1.0 CG C:LEU182 4.9 87.0 1.0 CD2 C:TYR206 4.9 77.2 1.0 CE C:MET93 5.0 89.6 1.0

H.R.Schmidt, R.M.Betz, R.O.Dror, A.C.Kruse. Structural Basis For SIGMA1RECEPTOR Ligand Recognition. Nat. Struct. Mol. Biol. V. 25 981 2018.
ISSN: ESSN 1545-9985
PubMed: 30291362
DOI: 10.1038/S41594-018-0137-2