Sodium in PDB 6f15: Glic Mutant H127Q

The structure of Glic Mutant H127Q, PDB code: 6f15 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 / 2.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.210, 133.100, 161.770, 90.00, 102.82, 90.00
R / Rfree (%)	20.1 / 22.9

The structure of Glic Mutant H127Q also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Glic Mutant H127Q (pdb code 6f15). 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 H127Q, PDB code: 6f15:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Glic Mutant H127Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glic Mutant H127Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:0.3 occ:1.00 O A:ILE71 2.9 0.1 1.0 N A:ILE73 3.2 91.1 1.0 CA A:TRP72 3.6 98.8 1.0 C A:TRP72 3.8 99.2 1.0 O A:PRO68 3.9 0.2 1.0 C A:ILE71 3.9 0.1 1.0 CG2 A:VAL5 3.9 0.2 1.0 CB A:ILE73 3.9 87.8 1.0 CA A:ILE73 4.1 86.8 1.0 O A:ILE73 4.1 90.0 1.0 N A:TRP72 4.2 0.1 1.0 CG1 A:ILE73 4.4 89.6 1.0 CD1 A:ILE73 4.5 94.8 1.0 C A:ILE73 4.6 89.2 1.0 CB A:TRP72 4.8 98.7 1.0 O A:TRP72 4.9 99.4 1.0

Sodium binding site 2 out of 6 in the Glic Mutant H127Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Glic Mutant H127Q within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:88.6 occ:1.00 O B:ILE71 2.8 94.6 1.0 N B:ILE73 3.4 85.2 1.0 CG2 B:VAL5 3.7 0.5 1.0 CA B:TRP72 3.7 93.3 1.0 O B:PRO68 3.8 0.6 1.0 C B:ILE71 3.8 96.5 1.0 C B:TRP72 4.0 95.2 1.0 N B:TRP72 4.2 94.2 1.0 CB B:ILE73 4.2 81.5 1.0 CA B:ILE73 4.4 80.3 1.0 O B:ILE73 4.4 81.3 1.0 CG1 B:ILE73 4.6 82.7 1.0 CD1 B:ILE73 4.7 90.2 1.0 C B:ILE73 4.9 82.1 1.0 C B:PRO68 4.9 0.5 1.0 O B:GLU69 4.9 0.3 1.0 CB B:TRP72 5.0 94.2 1.0

Sodium binding site 3 out of 6 in the Glic Mutant H127Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Glic Mutant H127Q within 5.0Å range: probe atom residue distance (Å) B Occ C:Na405 b:93.5 occ:1.00 O C:ILE71 2.7 98.6 1.0 O C:PRO68 3.0 0.7 1.0 C C:ILE71 3.8 0.1 1.0 N C:ILE73 3.9 91.2 1.0 C C:PRO68 4.1 0.2 1.0 CA C:TRP72 4.2 94.8 1.0 CG2 C:VAL5 4.2 0.6 1.0 CD1 C:ILE73 4.2 99.5 1.0 CB C:ILE73 4.2 89.4 1.0 C C:TRP72 4.4 98.5 1.0 CG1 C:ILE73 4.4 91.8 1.0 N C:TRP72 4.4 97.2 1.0 O C:GLU69 4.6 0.6 1.0 CA C:ILE73 4.7 87.1 1.0 CA C:GLU69 4.8 0.6 1.0 N C:GLU69 4.8 0.7 1.0 C C:GLU69 4.8 0.7 1.0 O C:ILE73 5.0 86.1 1.0

Sodium binding site 4 out of 6 in the Glic Mutant H127Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Glic Mutant H127Q within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:58.5 occ:1.00 OG1 D:THR226 3.7 32.6 1.0 OG1 C:THR226 4.0 34.0 1.0 OG1 E:THR226 4.2 37.6 1.0 OG1 A:THR226 4.6 37.1 1.0 OG1 B:THR226 4.7 35.0 1.0 CG2 C:THR226 4.9 31.8 1.0 CG2 D:THR226 4.9 17.0 1.0 CB D:THR226 4.9 21.9 1.0

Sodium binding site 5 out of 6 in the Glic Mutant H127Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Glic Mutant H127Q within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:0.8 occ:1.00 O D:ILE71 3.1 0.9 1.0 N D:ILE73 3.3 93.4 1.0 CG2 D:VAL5 3.6 0.7 1.0 CA D:TRP72 3.6 0.6 1.0 C D:TRP72 3.9 0.4 1.0 C D:ILE71 4.0 0.5 1.0 O D:ILE73 4.1 95.1 1.0 O D:PRO68 4.2 0.8 1.0 N D:TRP72 4.2 0.9 1.0 CB D:ILE73 4.2 91.1 1.0 CA D:ILE73 4.2 89.5 1.0 C D:ILE73 4.7 92.8 1.0 CB D:TRP72 4.8 0.6 1.0 CG1 D:ILE73 4.8 93.1 1.0 CD1 D:TRP72 4.9 0.1 1.0 CD1 D:ILE73 4.9 0.9 1.0 CG D:TRP72 4.9 99.8 1.0 CB D:VAL5 5.0 0.3 1.0

Sodium binding site 6 out of 6 in the Glic Mutant H127Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Glic Mutant H127Q within 5.0Å range: probe atom residue distance (Å) B Occ E:Na405 b:1.0 occ:1.00 O E:ILE71 2.4 0.1 1.0 O E:PRO68 2.8 0.3 1.0 N E:ILE73 3.1 88.5 1.0 CB E:ILE73 3.3 87.4 1.0 CD1 E:ILE73 3.3 95.4 1.0 CG1 E:ILE73 3.4 89.2 1.0 C E:ILE71 3.5 0.5 1.0 C E:TRP72 3.7 97.4 1.0 CA E:ILE73 3.8 84.6 1.0 CA E:TRP72 3.8 96.0 1.0 C E:PRO68 3.9 0.3 1.0 N E:TRP72 4.1 98.3 1.0 O E:ILE73 4.5 82.7 1.0 O E:TRP72 4.6 98.8 1.0 CG2 E:ILE73 4.6 86.2 1.0 C E:ILE73 4.7 83.6 1.0 CA E:PRO68 4.7 0.5 1.0 CA E:ILE71 4.8 0.7 1.0 CG2 E:VAL5 4.8 0.6 1.0 N E:ILE71 4.9 0.7 1.0 N E:GLU69 4.9 0.7 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