Sodium in PDB 5l47: X-Ray Structure of the 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate)

The structure of X-Ray Structure of the 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate), PDB code: 5l47 was solved by R.Reinholds Ruza, Z.Fourati, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.00 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	181.158, 128.124, 162.193, 90.00, 102.72, 90.00
R / Rfree (%)	21 / 23

The structure of X-Ray Structure of the 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate) also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the X-Ray Structure of the 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate) (pdb code 5l47). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of the 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate), PDB code: 5l47:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the X-Ray Structure of the 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate)


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 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:94.7 occ:1.00 O A:PRO68 3.3 0.5 1.0 O A:ILE71 3.3 89.0 1.0 O A:GLU69 4.2 0.3 1.0 C A:PRO68 4.3 0.9 1.0 CG1 A:VAL5 4.3 0.6 1.0 CA A:GLU69 4.3 98.5 1.0 C A:ILE71 4.4 88.3 1.0 C A:GLU69 4.5 0.1 1.0 N A:GLU69 4.7 98.7 1.0 N A:ILE73 5.0 79.2 1.0 CA A:TRP72 5.0 78.8 1.0

Sodium binding site 2 out of 4 in the X-Ray Structure of the 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate)


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 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:98.2 occ:1.00 O C:PRO68 3.0 74.1 1.0 O C:ILE71 3.1 72.7 1.0 C C:PRO68 4.0 76.7 1.0 O C:GLU69 4.0 76.1 1.0 CA C:GLU69 4.1 73.3 1.0 C C:ILE71 4.3 71.1 1.0 C C:GLU69 4.3 75.7 1.0 CG2 C:VAL5 4.3 0.8 1.0 N C:GLU69 4.5 74.0 1.0 N C:ILE73 4.8 61.7 1.0 CA C:TRP72 4.9 64.4 1.0 N C:ILE71 5.0 72.0 1.0

Sodium binding site 3 out of 4 in the X-Ray Structure of the 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate)


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 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na404 b:0.7 occ:1.00 O D:ILE71 3.5 80.8 1.0 O D:PRO68 3.7 97.7 1.0 CG1 D:VAL5 4.4 0.9 1.0 C D:ILE71 4.6 83.5 1.0 C D:PRO68 4.7 97.3 1.0 N D:ILE73 4.8 80.5 1.0 O D:GLU69 4.8 90.1 1.0 CA D:GLU69 4.8 92.0 1.0 CA D:TRP72 4.9 81.5 1.0

Sodium binding site 4 out of 4 in the X-Ray Structure of the 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate)


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 2-22' Locally-Closed Mutant of Glic in Complex with Cyanoselenobarbital (Seleniated Barbiturate) within 5.0Å range: probe atom residue distance (Å) B Occ E:Na403 b:82.3 occ:1.00 O E:ILE71 2.5 72.6 1.0 O E:PRO68 2.7 77.2 1.0 C E:ILE71 3.7 74.5 1.0 C E:PRO68 3.8 78.5 1.0 N E:ILE73 4.0 64.7 1.0 CA E:TRP72 4.3 69.1 1.0 CA E:GLU69 4.4 78.6 1.0 CB E:ILE73 4.4 64.8 1.0 O E:GLU69 4.4 85.5 1.0 N E:TRP72 4.5 69.8 1.0 C E:TRP72 4.5 72.4 1.0 CD1 E:ILE73 4.5 64.8 1.0 N E:GLU69 4.5 77.9 1.0 C E:GLU69 4.5 84.1 1.0 CG1 E:ILE73 4.6 63.9 1.0 N E:ILE71 4.7 76.3 1.0 CA E:ILE73 4.8 63.1 1.0 CA E:ILE71 4.9 74.6 1.0 CA E:PRO68 4.9 73.0 1.0 CG1 E:VAL5 4.9 0.4 1.0 O E:ILE73 5.0 66.2 1.0

Z.Fourati, R.R.Ruza, D.Laverty, E.Drege, S.Delarue-Cochin, D.Joseph, P.Koehl, T.Smart, M.Delarue. Barbiturates Bind in the Glic Ion Channel Pore and Cause Inhibition By Stabilizing A Closed State. J. Biol. Chem. V. 292 1550 2017.
ISSN: ESSN 1083-351X
PubMed: 27986812
DOI: 10.1074/JBC.M116.766964