Sodium in PDB 5mzr: X-Ray Structure of the H235Q Mutant of Glic in Complex with Propofol

The structure of X-Ray Structure of the H235Q Mutant of Glic in Complex with Propofol, PDB code: 5mzr was solved by 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 / 2.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.842, 132.989, 161.162, 90.00, 102.83, 90.00
R / Rfree (%)	19.1 / 21

The structure of X-Ray Structure of the H235Q Mutant of Glic in Complex with Propofol also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the X-Ray Structure of the H235Q Mutant of Glic in Complex with Propofol (pdb code 5mzr). 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 H235Q Mutant of Glic in Complex with Propofol, PDB code: 5mzr:
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 H235Q 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 H235Q Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:87.3 occ:1.00 O A:ILE71 2.5 83.8 1.0 O A:PRO68 3.1 0.2 1.0 C A:ILE71 3.6 85.4 1.0 N A:ILE73 3.7 76.5 1.0 CA A:TRP72 3.9 80.5 1.0 C A:PRO68 4.1 0.1 1.0 C A:TRP72 4.2 82.8 1.0 N A:TRP72 4.2 81.6 1.0 CB A:ILE73 4.2 76.6 1.0 CD1 A:ILE73 4.3 82.8 1.0 CG1 A:ILE73 4.3 76.9 1.0 CA A:ILE73 4.5 74.1 1.0 CA A:GLU69 4.6 0.7 1.0 O A:GLU69 4.7 0.5 1.0 N A:GLU69 4.8 0.1 1.0 C A:GLU69 4.8 0.5 1.0 CA A:ILE71 4.8 83.6 1.0 N A:ILE71 4.8 86.0 1.0 O A:ILE73 4.9 75.7 1.0

Sodium binding site 2 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:87.5 occ:1.00 OG1 B:THR226 3.9 75.7 1.0 OG1 C:THR226 4.0 75.0 1.0 OE2 B:GLU222 4.1 1.0 1.0 OG1 A:THR226 4.2 84.6 1.0 OG1 D:THR226 4.5 81.8 1.0 CG2 B:THR226 4.5 66.9 1.0 OE1 B:GLU222 4.5 1.0 1.0 OG1 E:THR226 4.5 76.1 1.0 CD B:GLU222 4.7 0.5 1.0 CG2 A:THR226 4.8 76.1 1.0 CG2 C:THR226 4.8 74.1 1.0 CB B:THR226 4.9 72.3 1.0 O E:HOH528 5.0 70.6 1.0

Sodium binding site 3 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:88.7 occ:1.00 O B:ILE71 2.4 76.0 1.0 O B:PRO68 3.0 94.2 1.0 C B:ILE71 3.6 77.5 1.0 N B:ILE73 3.7 66.8 1.0 CA B:TRP72 4.0 71.0 1.0 C B:PRO68 4.0 95.4 1.0 CD1 B:ILE73 4.1 72.9 1.0 CB B:ILE73 4.1 66.6 1.0 C B:TRP72 4.2 72.0 1.0 CG1 B:ILE73 4.2 67.5 1.0 N B:TRP72 4.2 72.5 1.0 CG2 B:VAL5 4.2 0.5 1.0 CA B:ILE73 4.5 64.3 1.0 CA B:GLU69 4.5 94.4 1.0 O B:GLU69 4.6 95.2 1.0 N B:GLU69 4.6 93.7 1.0 C B:GLU69 4.7 94.8 1.0 N B:ILE71 4.8 80.0 1.0 CA B:ILE71 4.8 77.3 1.0 O B:ILE73 4.9 70.5 1.0

Sodium binding site 4 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ C:Na406 b:82.9 occ:1.00 O C:ILE71 2.7 85.7 1.0 N C:ILE73 3.3 76.0 1.0 O C:PRO68 3.6 96.2 1.0 CA C:TRP72 3.7 80.3 1.0 C C:ILE71 3.8 86.9 1.0 C C:TRP72 3.9 82.7 1.0 CB C:ILE73 4.0 75.4 1.0 CA C:ILE73 4.2 73.3 1.0 CG1 C:ILE73 4.2 75.7 1.0 N C:TRP72 4.2 82.2 1.0 CD1 C:ILE73 4.3 83.4 1.0 O C:ILE73 4.4 76.8 1.0 C C:PRO68 4.7 97.3 1.0 C C:ILE73 4.8 77.0 1.0 CB C:TRP72 5.0 78.8 1.0 O C:TRP72 5.0 82.7 1.0

Sodium binding site 5 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:95.1 occ:1.00 O D:ILE71 2.6 83.6 1.0 O D:PRO68 3.2 0.3 1.0 N D:ILE73 3.5 77.2 1.0 C D:ILE71 3.7 84.8 1.0 CA D:TRP72 3.9 79.0 1.0 CB D:ILE73 4.0 78.1 1.0 C D:TRP72 4.1 82.2 1.0 CD1 D:ILE73 4.2 92.6 1.0 CG1 D:ILE73 4.2 79.5 1.0 C D:PRO68 4.2 0.9 1.0 N D:TRP72 4.3 80.6 1.0 CA D:ILE73 4.4 75.5 1.0 O D:ILE73 4.7 76.8 1.0 CA D:GLU69 4.8 0.5 1.0 O D:GLU69 4.8 0.1 1.0 N D:GLU69 4.9 0.2 1.0 C D:GLU69 4.9 0.0 1.0 CA D:ILE71 4.9 84.4 1.0 N D:ILE71 5.0 86.5 1.0

Sodium binding site 6 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Propofol within 5.0Å range: probe atom residue distance (Å) B Occ E:Na406 b:92.2 occ:1.00 O E:ILE71 2.8 86.2 1.0 O E:PRO68 3.4 0.4 1.0 N E:ILE73 3.6 76.5 1.0 C E:ILE71 3.9 88.5 1.0 CA E:TRP72 4.0 81.7 1.0 CB E:ILE73 4.1 75.3 1.0 C E:TRP72 4.2 83.4 1.0 CD1 E:ILE73 4.3 80.9 1.0 CG1 E:ILE73 4.3 75.7 1.0 N E:TRP72 4.4 83.5 1.0 C E:PRO68 4.4 0.1 1.0 CA E:ILE73 4.5 73.3 1.0 O E:ILE73 4.7 75.7 1.0 CA E:GLU69 4.9 0.9 1.0

Z.Fourati, M.Delarue. X-Ray Structure of the H235Q Mutant of Glic in Complex with Propofol To Be Published.