Sodium in PDB 5iux: Glic-V135C Bimane Labelled X-Ray Structure

The structure of Glic-V135C Bimane Labelled X-Ray Structure, PDB code: 5iux was solved by Z.Fourati, A.Menny, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.034, 134.075, 159.945, 90.00, 102.51, 90.00
R / Rfree (%)	20.3 / 23.7

The structure of Glic-V135C Bimane Labelled X-Ray Structure also contains other interesting chemical elements:

Bromine

(Br)

5 atoms

The binding sites of Sodium atom in the Glic-V135C Bimane Labelled X-Ray Structure (pdb code 5iux). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Glic-V135C Bimane Labelled X-Ray Structure, PDB code: 5iux:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Glic-V135C Bimane Labelled X-Ray Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glic-V135C Bimane Labelled X-Ray Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:0.5 occ:1.00 O B:ILE71 2.4 86.8 1.0 O B:PRO68 3.2 0.9 1.0 N B:ILE73 3.4 77.6 1.0 C B:ILE71 3.6 84.6 1.0 CB B:ILE73 3.9 78.1 1.0 CA B:TRP72 3.9 75.4 1.0 C B:TRP72 4.0 82.0 1.0 CD1 B:ILE73 4.0 86.2 1.0 CG1 B:ILE73 4.2 78.7 1.0 N B:TRP72 4.2 77.7 1.0 CA B:ILE73 4.2 75.6 1.0 C B:PRO68 4.3 0.8 1.0 O B:ILE73 4.7 77.5 1.0 O B:GLU69 4.7 97.7 1.0 CA B:GLU69 4.8 96.6 1.0 CA B:ILE71 4.8 81.5 1.0 N B:ILE71 4.9 83.1 1.0 CG1 B:VAL5 4.9 0.4 1.0 CG2 B:VAL5 4.9 0.4 1.0 C B:GLU69 4.9 97.8 1.0 N B:GLU69 5.0 97.2 1.0 O B:TRP72 5.0 82.8 1.0 C B:ILE73 5.0 78.5 1.0

Sodium binding site 2 out of 4 in the Glic-V135C Bimane Labelled X-Ray Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Glic-V135C Bimane Labelled X-Ray Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Na606 b:90.4 occ:1.00 O C:ILE71 2.6 99.8 1.0 O C:PRO68 2.8 0.7 1.0 C C:ILE71 3.7 99.7 1.0 C C:PRO68 3.9 0.8 1.0 N C:ILE73 3.9 91.8 1.0 O C:GLU69 4.0 0.8 1.0 CD1 C:ILE73 4.0 97.8 1.0 CA C:TRP72 4.1 93.1 1.0 CA C:GLU69 4.2 0.5 1.0 C C:GLU69 4.3 0.6 1.0 N C:TRP72 4.4 94.2 1.0 CB C:ILE73 4.4 91.9 1.0 C C:TRP72 4.4 96.9 1.0 N C:GLU69 4.5 0.9 1.0 CG1 C:VAL5 4.6 0.9 1.0 CG1 C:ILE73 4.7 91.8 1.0 CA C:ILE73 4.8 89.6 1.0 N C:ILE71 4.8 98.8 1.0 CA C:ILE71 4.9 98.1 1.0 CB C:VAL5 4.9 0.1 1.0 CA C:PRO68 5.0 0.3 1.0

Sodium binding site 3 out of 4 in the Glic-V135C Bimane Labelled X-Ray Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Glic-V135C Bimane Labelled X-Ray Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Na606 b:0.3 occ:1.00 O D:ILE71 2.6 99.9 1.0 N D:ILE73 3.4 92.5 1.0 CG2 D:VAL5 3.5 0.1 1.0 O D:PRO68 3.5 0.9 1.0 CA D:TRP72 3.7 91.7 1.0 C D:ILE71 3.7 99.8 1.0 C D:TRP72 4.0 97.1 1.0 N D:TRP72 4.1 93.7 1.0 CB D:ILE73 4.2 94.1 1.0 CA D:ILE73 4.3 90.9 1.0 C D:PRO68 4.5 0.5 1.0 O D:ILE73 4.6 89.9 1.0 O D:GLU69 4.7 0.8 1.0 CD1 D:ILE73 4.8 0.6 1.0 CB D:VAL5 4.8 0.2 1.0 CA D:GLU69 4.8 0.5 1.0 CB D:TRP72 4.9 88.5 1.0 CG1 D:ILE73 4.9 94.5 1.0 C D:GLU69 5.0 0.2 1.0

Sodium binding site 4 out of 4 in the Glic-V135C Bimane Labelled X-Ray Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Glic-V135C Bimane Labelled X-Ray Structure within 5.0Å range: probe atom residue distance (Å) B Occ E:Na408 b:0.7 occ:1.00 O E:ILE71 2.6 1.0 1.0 O E:PRO68 3.1 0.2 1.0 CG2 E:VAL5 3.6 0.2 1.0 C E:ILE71 3.7 0.2 1.0 N E:ILE73 3.9 98.2 1.0 CA E:TRP72 4.1 98.0 1.0 C E:PRO68 4.1 0.0 1.0 O E:GLU69 4.3 0.6 1.0 N E:TRP72 4.4 98.7 1.0 C E:TRP72 4.4 0.8 1.0 CA E:GLU69 4.4 0.9 1.0 CD1 E:ILE73 4.4 0.7 1.0 CB E:ILE73 4.5 99.2 1.0 CG1 E:ILE73 4.6 99.1 1.0 C E:GLU69 4.6 0.8 1.0 N E:GLU69 4.7 0.2 1.0 CB E:VAL5 4.8 0.2 1.0 CA E:ILE73 4.8 96.4 1.0 N E:ILE71 4.9 0.2 1.0 CA E:ILE71 4.9 0.0 1.0

A.Menny, S.N.Lefebvre, P.A.Schmidpeter, E.Drege, Z.Fourati, M.Delarue, S.J.Edelstein, C.M.Nimigean, D.Joseph, P.J.Corringer. Identification of A Pre-Active Conformation of A Pentameric Channel Receptor. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28294942
DOI: 10.7554/ELIFE.23955