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

Protein crystallography data

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

Other elements in 6djz:

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

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

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 6djz

Go back to Fluorine Binding Sites List in 6djz
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 6djz

Go back to Fluorine Binding Sites List in 6djz
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 6djz

Go back to Fluorine Binding Sites List in 6djz
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

Reference:

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
Page generated: Sun Dec 13 12:48:02 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy