Sodium in PDB 6f0n: Glic Mutant E82A

The structure of Glic Mutant E82A, PDB code: 6f0n was solved by H.D.Hu, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.220, 132.600, 159.030, 90.00, 101.65, 90.00
R / Rfree (%)	21 / 23.3

The structure of Glic Mutant E82A also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Glic Mutant E82A (pdb code 6f0n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Glic Mutant E82A, PDB code: 6f0n:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Glic Mutant E82A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glic Mutant E82A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:78.5 occ:1.00 O A:ILE71 2.3 87.4 1.0 O A:PRO68 2.7 0.2 1.0 C A:ILE71 3.5 88.2 1.0 N A:ILE73 3.6 75.1 1.0 C A:PRO68 3.9 0.1 1.0 CB A:ILE73 4.0 75.1 1.0 CA A:TRP72 4.0 80.9 1.0 CD1 A:ILE73 4.0 82.2 1.0 C A:TRP72 4.1 81.9 1.0 CG1 A:ILE73 4.1 75.5 1.0 N A:TRP72 4.2 82.7 1.0 CG2 A:VAL5 4.3 97.7 1.0 CA A:ILE73 4.4 72.3 1.0 O A:GLU69 4.5 96.1 1.0 CA A:GLU69 4.6 95.2 1.0 C A:GLU69 4.6 96.7 1.0 N A:GLU69 4.6 95.9 1.0 N A:ILE71 4.6 89.7 1.0 CA A:ILE71 4.7 88.0 1.0 O A:ILE73 4.9 71.0 1.0 CA A:PRO68 4.9 95.6 1.0

Sodium binding site 2 out of 6 in the Glic Mutant E82A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Glic Mutant E82A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:78.4 occ:1.00 O B:ILE71 3.0 82.5 1.0 O B:PRO68 3.2 99.1 1.0 N B:ILE73 3.9 75.1 1.0 C B:ILE71 4.1 84.2 1.0 C B:PRO68 4.3 99.0 1.0 CG2 B:VAL5 4.3 0.7 1.0 CB B:ILE73 4.3 75.5 1.0 CA B:TRP72 4.4 79.1 1.0 C B:TRP72 4.5 82.0 1.0 CD1 B:ILE73 4.6 84.0 1.0 O B:GLU69 4.7 99.5 1.0 CA B:ILE73 4.7 72.5 1.0 CG1 B:ILE73 4.7 76.1 1.0 N B:TRP72 4.7 80.2 1.0 CA B:GLU69 4.7 95.9 1.0 O B:ILE73 4.9 70.9 1.0 N B:GLU69 4.9 96.0 1.0 C B:GLU69 4.9 98.5 1.0

Sodium binding site 3 out of 6 in the Glic Mutant E82A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Glic Mutant E82A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:75.0 occ:1.00 O C:ILE71 2.5 91.0 1.0 O C:PRO68 2.8 96.1 1.0 N C:ILE73 3.7 78.9 1.0 C C:ILE71 3.7 93.0 1.0 C C:PRO68 3.9 96.2 1.0 CB C:ILE73 4.0 77.9 1.0 CD1 C:ILE73 4.1 83.8 1.0 CA C:TRP72 4.2 85.9 1.0 CG1 C:ILE73 4.3 78.1 1.0 C C:TRP72 4.3 85.8 1.0 N C:TRP72 4.4 87.7 1.0 CG2 C:VAL5 4.4 0.2 1.0 CA C:ILE73 4.5 76.0 1.0 O C:GLU69 4.5 99.5 1.0 CA C:GLU69 4.5 94.0 1.0 N C:GLU69 4.6 93.4 1.0 C C:GLU69 4.7 98.7 1.0 N C:ILE71 4.8 93.8 1.0 CA C:ILE71 4.9 93.0 1.0 O C:ILE73 4.9 78.6 1.0 CA C:PRO68 4.9 90.6 1.0

Sodium binding site 4 out of 6 in the Glic Mutant E82A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Glic Mutant E82A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:81.5 occ:1.00 OG1 D:THR226 3.3 69.3 1.0 OG1 C:THR226 3.7 81.5 1.0 CG2 C:THR226 4.2 74.3 1.0 OG1 E:THR226 4.3 74.7 1.0 CG2 D:THR226 4.3 59.6 1.0 CB D:THR226 4.4 65.2 1.0 CB C:THR226 4.6 77.7 1.0

Sodium binding site 5 out of 6 in the Glic Mutant E82A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Glic Mutant E82A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na405 b:99.2 occ:1.00 O D:ILE71 2.6 90.0 1.0 O D:PRO68 2.9 95.6 1.0 C D:ILE71 3.8 90.3 1.0 N D:ILE73 3.9 77.4 1.0 C D:PRO68 4.0 96.2 1.0 CG2 D:VAL5 4.1 0.2 1.0 CA D:TRP72 4.2 84.5 1.0 O D:GLU69 4.3 96.2 1.0 CB D:ILE73 4.4 77.4 1.0 CA D:GLU69 4.4 93.4 1.0 CD1 D:ILE73 4.4 85.8 1.0 C D:TRP72 4.4 84.9 1.0 N D:TRP72 4.4 85.7 1.0 C D:GLU69 4.5 96.0 1.0 CG1 D:ILE73 4.6 77.9 1.0 N D:GLU69 4.6 93.5 1.0 CA D:ILE73 4.7 74.7 1.0 N D:ILE71 4.8 89.3 1.0 CA D:ILE71 4.9 87.7 1.0

Sodium binding site 6 out of 6 in the Glic Mutant E82A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Glic Mutant E82A within 5.0Å range: probe atom residue distance (Å) B Occ E:Na404 b:0.7 occ:1.00 O E:ILE71 2.3 89.0 1.0 O E:PRO68 2.8 99.3 1.0 C E:ILE71 3.5 90.1 1.0 N E:ILE73 3.8 78.4 1.0 C E:PRO68 3.9 99.8 1.0 CA E:TRP72 4.1 83.6 1.0 CG2 E:VAL5 4.1 0.2 1.0 N E:TRP72 4.2 85.0 1.0 O E:GLU69 4.2 0.4 1.0 CD1 E:ILE73 4.3 82.8 1.0 C E:TRP72 4.3 84.5 1.0 CB E:ILE73 4.3 78.1 1.0 CA E:GLU69 4.4 97.6 1.0 C E:GLU69 4.4 99.9 1.0 CG1 E:ILE73 4.5 77.9 1.0 N E:GLU69 4.5 97.2 1.0 N E:ILE71 4.6 90.8 1.0 CA E:ILE71 4.6 88.9 1.0 CA E:ILE73 4.7 75.6 1.0 CA E:PRO68 5.0 94.6 1.0

A.Nemecz, H.Hu, Z.Fourati, C.Van Renterghem, M.Delarue, P.J.Corringer. Full Mutational Mapping of Titratable Residues Helps to Identify Proton-Sensors Involved in the Control of Channel Gating in the Gloeobacter Violaceus Pentameric Ligand-Gated Ion Channel. Plos Biol. V. 15 04470 2017.
ISSN: ESSN 1545-7885
PubMed: 29281623
DOI: 10.1371/JOURNAL.PBIO.2004470