Sodium in PDB 6f13: Glic Mutant E75A

The structure of Glic Mutant E75A, PDB code: 6f13 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)	49.10 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	179.948, 132.450, 159.234, 90.00, 101.95, 90.00
R / Rfree (%)	20.3 / 22.3

The structure of Glic Mutant E75A also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Glic Mutant E75A (pdb code 6f13). 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 E75A, PDB code: 6f13:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Glic Mutant E75A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glic Mutant E75A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:82.7 occ:1.00 O A:ILE71 2.4 70.4 1.0 N A:ILE73 3.2 67.6 1.0 O A:PRO68 3.3 83.6 1.0 C A:ILE71 3.6 72.7 1.0 CA A:TRP72 3.7 69.4 1.0 CB A:ILE73 3.8 67.6 1.0 C A:TRP72 3.8 72.4 1.0 CG1 A:ILE73 3.9 68.4 1.0 CD1 A:ILE73 4.0 73.2 1.0 CA A:ILE73 4.0 65.4 1.0 N A:TRP72 4.1 70.2 1.0 C A:PRO68 4.4 84.0 1.0 O A:ILE73 4.4 65.0 1.0 C A:ILE73 4.8 66.4 1.0 O A:TRP72 4.8 72.4 1.0 CA A:ILE71 4.9 71.6 1.0

Sodium binding site 2 out of 6 in the Glic Mutant E75A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Glic Mutant E75A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:94.8 occ:1.00 O B:HOH542 4.1 62.6 1.0 OG1 A:THR226 4.2 61.2 1.0 OG1 E:THR226 4.2 58.7 1.0 OG1 C:THR226 4.2 63.9 1.0 OG1 B:THR226 4.3 61.1 1.0 OG1 D:THR226 4.3 57.9 1.0

Sodium binding site 3 out of 6 in the Glic Mutant E75A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Glic Mutant E75A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:71.3 occ:1.00 O B:ILE71 2.6 67.7 1.0 O B:PRO68 3.4 82.4 1.0 N B:ILE73 3.6 64.7 1.0 C B:ILE71 3.8 68.8 1.0 CA B:TRP72 4.0 64.8 1.0 CB B:ILE73 4.1 64.9 1.0 C B:TRP72 4.2 70.2 1.0 CD1 B:ILE73 4.3 77.0 1.0 CG1 B:ILE73 4.3 66.5 1.0 N B:TRP72 4.3 65.3 1.0 CA B:ILE73 4.4 62.5 1.0 C B:PRO68 4.4 82.8 1.0 O B:ILE73 4.6 68.1 1.0 CG1 B:VAL5 4.7 99.9 1.0

Sodium binding site 4 out of 6 in the Glic Mutant E75A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Glic Mutant E75A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na406 b:74.5 occ:1.00 O C:ILE71 2.7 78.2 1.0 N C:ILE73 3.3 70.0 1.0 O C:PRO68 3.6 84.2 1.0 CA C:TRP72 3.8 73.1 1.0 C C:ILE71 3.8 78.5 1.0 CB C:ILE73 3.9 68.7 1.0 C C:TRP72 3.9 75.9 1.0 CA C:ILE73 4.1 67.1 1.0 CG1 C:ILE73 4.2 69.5 1.0 N C:TRP72 4.3 73.5 1.0 O C:ILE73 4.3 69.6 1.0 CD1 C:ILE73 4.3 76.7 1.0 CG1 C:VAL5 4.6 94.3 1.0 C C:PRO68 4.7 83.8 1.0 C C:ILE73 4.7 70.8 1.0

Sodium binding site 5 out of 6 in the Glic Mutant E75A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Glic Mutant E75A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:0.0 occ:1.00 O D:ILE71 2.5 73.6 1.0 O D:PRO68 3.3 87.5 1.0 N D:ILE73 3.5 65.2 1.0 C D:ILE71 3.7 75.9 1.0 CA D:TRP72 3.9 70.7 1.0 CB D:ILE73 4.0 66.1 1.0 C D:TRP72 4.1 71.9 1.0 CD1 D:ILE73 4.2 75.3 1.0 CG1 D:ILE73 4.2 67.5 1.0 N D:TRP72 4.2 72.1 1.0 C D:PRO68 4.3 87.5 1.0 CA D:ILE73 4.3 63.8 1.0 O D:ILE73 4.7 67.5 1.0 O D:GLU69 4.9 85.3 1.0 CA D:ILE71 4.9 75.5 1.0 CA D:GLU69 5.0 84.2 1.0

Sodium binding site 6 out of 6 in the Glic Mutant E75A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Glic Mutant E75A within 5.0Å range: probe atom residue distance (Å) B Occ E:Na405 b:87.8 occ:1.00 O E:ILE71 2.8 82.6 1.0 N E:ILE73 3.4 72.0 1.0 O E:PRO68 3.6 88.2 1.0 C E:ILE71 3.9 82.6 1.0 CA E:TRP72 3.9 76.8 1.0 CB E:ILE73 4.0 71.6 1.0 C E:TRP72 4.0 77.8 1.0 CA E:ILE73 4.2 69.2 1.0 CG2 E:VAL5 4.2 95.2 1.0 CG1 E:ILE73 4.3 73.1 1.0 CD1 E:ILE73 4.3 83.2 1.0 O E:ILE73 4.3 70.6 1.0 N E:TRP72 4.4 78.2 1.0 C E:PRO68 4.7 88.9 1.0 C E:ILE73 4.8 71.3 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