Chlorine 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:

Fluorine

(F)

3 atoms

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

Chlorine 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 Chlorine with other atoms in the Cl binding site number 1 of Human Sigma-1 Receptor Bound to Haloperidol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:0.3 occ:1.00 CL1 A:GMJ301 0.0 0.3 1.0 C21 A:GMJ301 1.8 0.1 1.0 C22 A:GMJ301 2.7 0.3 1.0 C20 A:GMJ301 2.8 0.6 1.0 NE2 A:GLN135 3.1 0.6 1.0 CG2 A:VAL152 3.5 0.3 1.0 O A:VAL153 3.5 0.9 1.0 ND1 A:HIS154 3.5 0.9 1.0 CB A:HIS154 3.7 97.1 1.0 C A:VAL153 3.8 0.7 1.0 CD A:GLN135 3.9 0.8 1.0 CA A:HIS154 3.9 90.8 1.0 CG A:HIS154 3.9 0.5 1.0 N A:HIS154 3.9 88.5 1.0 C23 A:GMJ301 4.0 0.4 1.0 C19 A:GMJ301 4.1 0.8 1.0 CG A:GLN135 4.5 93.2 1.0 OG1 A:THR160 4.5 0.3 1.0 N A:VAL153 4.5 87.8 1.0 CZ A:PHE133 4.5 95.6 1.0 C18 A:GMJ301 4.6 94.3 1.0 CE1 A:PHE133 4.6 98.6 1.0 CE1 A:HIS154 4.6 0.3 1.0 OE1 A:GLN135 4.6 0.9 1.0 CB A:VAL152 4.7 81.5 1.0 CG1 A:VAL152 4.7 77.7 1.0 C A:VAL152 4.7 81.7 1.0 CA A:VAL153 4.7 96.6 1.0 O A:VAL152 5.0 89.5 1.0

Chlorine 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 Chlorine with other atoms in the Cl binding site number 2 of Human Sigma-1 Receptor Bound to Haloperidol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:1.0 occ:1.00 CL1 B:GMJ301 0.0 1.0 1.0 C21 B:GMJ301 1.8 0.6 1.0 C22 B:GMJ301 2.7 0.3 1.0 C20 B:GMJ301 2.8 0.4 1.0 NE2 B:GLN135 3.0 0.5 1.0 CG1 B:VAL152 3.3 98.0 1.0 CD B:GLN135 3.7 0.7 1.0 CB B:HIS154 3.8 0.9 1.0 ND1 B:HIS154 3.8 0.0 1.0 CZ B:PHE133 4.0 0.9 1.0 CE1 B:PHE133 4.0 0.0 1.0 C19 B:GMJ301 4.0 0.8 1.0 C23 B:GMJ301 4.0 0.2 1.0 CG B:HIS154 4.1 0.9 1.0 CB B:VAL152 4.2 91.8 1.0 CG B:GLN135 4.3 97.1 1.0 OE1 B:GLN135 4.4 0.8 1.0 CA B:HIS154 4.4 0.4 1.0 O B:VAL153 4.5 0.9 1.0 OG1 B:THR160 4.5 0.4 1.0 C18 B:GMJ301 4.5 1.0 1.0 N B:HIS154 4.6 0.5 1.0 C B:VAL153 4.6 0.0 1.0 CE1 B:HIS154 4.8 0.3 1.0 C B:VAL152 4.8 96.5 1.0 O B:VAL152 5.0 0.7 1.0 N B:VAL153 5.0 0.8 1.0

Chlorine 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 Chlorine with other atoms in the Cl binding site number 3 of Human Sigma-1 Receptor Bound to Haloperidol within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl301 b:0.8 occ:1.00 CL1 C:GMJ301 0.0 0.8 1.0 C21 C:GMJ301 1.8 0.3 1.0 C22 C:GMJ301 2.7 0.8 1.0 C20 C:GMJ301 2.8 0.2 1.0 NE2 C:GLN135 3.2 0.4 1.0 CG1 C:VAL152 3.7 88.7 1.0 CB C:HIS154 3.7 0.9 1.0 ND1 C:HIS154 3.8 0.7 1.0 CZ C:PHE133 3.8 0.2 1.0 CG C:HIS154 4.0 0.6 1.0 C23 C:GMJ301 4.0 0.2 1.0 C19 C:GMJ301 4.0 0.4 1.0 OG1 C:THR160 4.2 77.5 1.0 CE1 C:PHE133 4.3 95.8 1.0 CD C:GLN135 4.3 0.8 1.0 CB C:VAL152 4.5 78.8 1.0 CG1 C:VAL162 4.5 89.6 1.0 C18 C:GMJ301 4.6 0.1 1.0 CA C:HIS154 4.6 85.8 1.0 CE1 C:HIS154 4.8 0.8 1.0 N C:HIS154 4.8 81.4 1.0 CE2 C:PHE133 4.8 0.7 1.0 O C:VAL153 4.8 0.9 1.0 C C:VAL153 4.9 94.8 1.0 CG C:GLN135 4.9 86.0 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