Sodium in PDB 5mur: X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol

The structure of X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol, PDB code: 5mur was solved by L.Sauguet, Z.Fourati, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.281, 132.972, 158.976, 90.00, 102.10, 90.00
R / Rfree (%)	19.4 / 20.4

The structure of X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol (pdb code 5mur). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol, PDB code: 5mur:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:0.1 occ:1.00 O A:ILE71 2.5 0.7 1.0 O A:PRO68 3.1 0.7 1.0 C A:ILE71 3.6 0.4 1.0 CA A:TRP72 4.0 1.0 1.0 N A:ILE73 4.0 95.5 1.0 C A:PRO68 4.2 0.0 1.0 N A:TRP72 4.2 0.8 1.0 CG1 A:VAL5 4.3 0.2 1.0 O A:GLU69 4.3 0.6 1.0 CA A:GLU69 4.4 0.5 1.0 C A:TRP72 4.4 1.0 1.0 C A:GLU69 4.5 0.5 1.0 CD1 A:ILE73 4.7 0.3 1.0 N A:GLU69 4.7 0.5 1.0 N A:ILE71 4.7 0.3 1.0 CA A:ILE71 4.8 0.6 1.0 CB A:ILE73 4.8 94.9 1.0 CG1 A:ILE73 5.0 95.8 1.0

Sodium binding site 2 out of 6 in the X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:0.4 occ:1.00 O B:ILE71 2.5 91.9 1.0 O B:PRO68 3.2 98.5 1.0 N B:ILE73 3.4 83.6 1.0 C B:ILE71 3.6 92.5 1.0 CA B:TRP72 3.8 87.9 1.0 C B:TRP72 4.0 89.4 1.0 CB B:ILE73 4.1 84.0 1.0 N B:TRP72 4.2 88.5 1.0 CD1 B:ILE73 4.2 93.8 1.0 CA B:ILE73 4.3 81.6 1.0 C B:PRO68 4.4 99.4 1.0 CG1 B:ILE73 4.4 84.7 1.0 O B:ILE73 4.6 83.7 1.0 CG1 B:VAL5 4.8 1.0 1.0 CA B:GLU69 4.9 97.8 1.0 O B:GLU69 4.9 99.8 1.0 CA B:ILE71 4.9 89.6 1.0

Sodium binding site 3 out of 6 in the X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:97.1 occ:1.00 OG1 B:THR226 3.9 0.3 1.0 OG1 C:THR226 4.2 0.9 1.0 OG1 A:THR226 4.4 0.6 1.0 CG2 B:THR226 4.4 98.5 1.0 CG2 A:THR226 4.7 0.6 1.0 OG1 D:THR226 4.8 0.1 1.0 CG2 C:THR226 4.8 0.5 1.0 CB B:THR226 4.8 0.5 1.0 OG1 E:THR226 4.9 0.4 1.0

Sodium binding site 4 out of 6 in the X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:0.0 occ:1.00 O C:ILE71 2.4 0.6 1.0 O C:PRO68 2.7 0.6 1.0 C C:ILE71 3.6 0.8 1.0 C C:PRO68 3.8 0.2 1.0 N C:ILE73 4.0 90.7 1.0 CA C:TRP72 4.1 96.8 1.0 CD1 C:ILE73 4.2 95.9 1.0 CA C:GLU69 4.2 0.9 1.0 N C:TRP72 4.3 98.2 1.0 O C:GLU69 4.3 1.0 1.0 C C:GLU69 4.4 0.8 1.0 N C:GLU69 4.4 0.4 1.0 C C:TRP72 4.4 97.5 1.0 CB C:ILE73 4.5 90.1 1.0 CG1 C:ILE73 4.6 90.8 1.0 N C:ILE71 4.7 0.4 1.0 CG1 C:VAL5 4.7 0.2 1.0 CA C:ILE71 4.7 0.2 1.0 CA C:ILE73 4.9 88.2 1.0 CA C:PRO68 4.9 0.3 1.0

Sodium binding site 5 out of 6 in the X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ D:Na403 b:0.2 occ:1.00 O D:ILE71 2.5 0.9 1.0 CG2 D:VAL5 3.2 0.9 1.0 C D:ILE71 3.5 0.2 1.0 CA D:TRP72 3.5 0.7 1.0 N D:ILE73 3.7 99.7 1.0 O D:PRO68 3.7 0.7 1.0 N D:TRP72 3.9 0.5 1.0 C D:TRP72 4.1 0.2 1.0 CB D:VAL5 4.5 0.2 1.0 CB D:TRP72 4.7 0.9 1.0 O D:GLU69 4.7 0.4 1.0 CB D:ILE73 4.7 99.7 1.0 CA D:ILE73 4.8 97.4 1.0 C D:PRO68 4.8 0.9 1.0 CA D:ILE71 4.8 1.0 1.0 CD1 D:ILE73 4.9 0.9 1.0 O D:ILE73 4.9 98.5 1.0 N D:ILE71 5.0 0.2 1.0 C D:GLU69 5.0 0.4 1.0

Sodium binding site 6 out of 6 in the X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Structure of the F14'A Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ E:Na404 b:0.4 occ:1.00 O E:ILE71 2.7 0.2 1.0 O E:PRO68 3.0 0.3 1.0 N E:ILE73 3.7 94.2 1.0 C E:ILE71 3.8 0.3 1.0 C E:PRO68 4.1 0.1 1.0 CA E:TRP72 4.1 0.8 1.0 CD1 E:ILE73 4.2 99.7 1.0 CB E:ILE73 4.3 93.7 1.0 C E:TRP72 4.3 0.7 1.0 N E:TRP72 4.4 0.9 1.0 CG1 E:ILE73 4.5 94.2 1.0 CA E:ILE73 4.6 91.6 1.0 CA E:GLU69 4.6 0.1 1.0 N E:GLU69 4.7 0.2 1.0 O E:GLU69 4.8 0.7 1.0 C E:GLU69 4.8 1.0 1.0 O E:ILE73 4.9 94.9 1.0 CG1 E:VAL5 4.9 0.7 1.0

Z.Fourati, R.J.Howard, S.A.Heusser, H.Hu, R.R.Ruza, L.Sauguet, E.Lindahl, M.Delarue. Structural Basis For A Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels. Cell Rep V. 23 993 2018.
ISSN: ESSN 2211-1247
PubMed: 29694907
DOI: 10.1016/J.CELREP.2018.03.108