Sodium in PDB 6f16: Glic Mutant H277Q

The structure of Glic Mutant H277Q, PDB code: 6f16 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)	21.30 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.700, 132.780, 161.550, 90.00, 102.96, 90.00
R / Rfree (%)	20.1 / 21.9

The structure of Glic Mutant H277Q also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Glic Mutant H277Q (pdb code 6f16). 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 H277Q, PDB code: 6f16:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Glic Mutant H277Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glic Mutant H277Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:67.7 occ:1.00 O A:ILE71 2.5 50.0 1.0 N A:ILE73 3.5 42.7 1.0 O A:PRO68 3.6 64.3 1.0 C A:ILE71 3.6 50.5 1.0 CA A:TRP72 3.8 45.2 1.0 C A:TRP72 4.0 49.7 1.0 CG2 A:VAL5 4.1 70.2 1.0 CB A:ILE73 4.1 41.7 1.0 N A:TRP72 4.2 46.5 1.0 CG1 A:ILE73 4.2 43.0 1.0 CA A:ILE73 4.4 40.0 1.0 CD1 A:ILE73 4.5 52.8 1.0 C A:PRO68 4.6 64.4 1.0 O A:ILE73 4.6 42.1 1.0 CA A:ILE71 4.9 49.5 1.0

Sodium binding site 2 out of 6 in the Glic Mutant H277Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Glic Mutant H277Q within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:60.1 occ:1.00 O B:ILE71 2.6 40.8 1.0 N B:ILE73 3.4 35.2 1.0 O B:PRO68 3.7 51.5 1.0 C B:ILE71 3.7 40.5 1.0 CA B:TRP72 3.8 36.1 1.0 C B:TRP72 4.0 41.6 1.0 CB B:ILE73 4.0 34.3 1.0 CG2 B:VAL5 4.1 80.5 1.0 CG1 B:ILE73 4.1 35.2 1.0 N B:TRP72 4.2 36.3 1.0 CA B:ILE73 4.3 32.8 1.0 CD1 B:ILE73 4.4 45.0 1.0 O B:ILE73 4.5 38.1 1.0 C B:PRO68 4.7 51.4 1.0 C B:ILE73 4.9 37.8 1.0 CA B:ILE71 5.0 38.0 1.0

Sodium binding site 3 out of 6 in the Glic Mutant H277Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Glic Mutant H277Q within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:70.0 occ:1.00 OG1 C:THR226 3.8 36.7 1.0 OG1 D:THR226 4.1 38.2 1.0 OG1 B:THR226 4.2 35.3 1.0 OG1 E:THR226 4.5 43.9 1.0 OG1 A:THR226 4.6 36.7 1.0 CG2 C:THR226 4.7 26.5 1.0 CB C:THR226 4.9 33.9 1.0

Sodium binding site 4 out of 6 in the Glic Mutant H277Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Glic Mutant H277Q within 5.0Å range: probe atom residue distance (Å) B Occ C:Na406 b:61.1 occ:1.00 O C:ILE71 2.6 50.3 1.0 N C:ILE73 3.5 43.8 1.0 O C:PRO68 3.5 57.3 1.0 C C:ILE71 3.7 50.8 1.0 CA C:TRP72 3.8 44.2 1.0 C C:TRP72 4.0 48.9 1.0 CB C:ILE73 4.0 42.8 1.0 CG2 C:VAL5 4.1 74.8 1.0 CG1 C:ILE73 4.1 43.6 1.0 N C:TRP72 4.2 45.6 1.0 CA C:ILE73 4.3 41.0 1.0 CD1 C:ILE73 4.4 52.7 1.0 O C:ILE73 4.6 44.9 1.0 C C:PRO68 4.6 57.5 1.0 CA C:ILE71 4.9 49.8 1.0 C C:ILE73 5.0 45.0 1.0

Sodium binding site 5 out of 6 in the Glic Mutant H277Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Glic Mutant H277Q within 5.0Å range: probe atom residue distance (Å) B Occ D:Na404 b:78.8 occ:1.00 O D:ILE71 2.8 51.4 1.0 N D:ILE73 3.3 42.2 1.0 O D:PRO68 3.7 65.7 1.0 CB D:ILE73 3.8 42.0 1.0 C D:ILE71 3.9 52.9 1.0 CA D:TRP72 3.9 47.6 1.0 C D:TRP72 4.0 50.1 1.0 CG1 D:ILE73 4.0 43.9 1.0 CA D:ILE73 4.1 39.8 1.0 O D:ILE73 4.3 40.6 1.0 N D:TRP72 4.3 48.9 1.0 CD1 D:ILE73 4.4 51.7 1.0 CG2 D:VAL5 4.4 75.9 1.0 C D:ILE73 4.7 42.0 1.0 C D:PRO68 4.8 66.1 1.0

Sodium binding site 6 out of 6 in the Glic Mutant H277Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Glic Mutant H277Q within 5.0Å range: probe atom residue distance (Å) B Occ E:Na405 b:60.0 occ:1.00 O E:ILE71 2.5 52.6 1.0 O E:PRO68 3.3 61.3 1.0 N E:ILE73 3.7 42.9 1.0 C E:ILE71 3.7 52.8 1.0 CA E:TRP72 4.0 43.9 1.0 CB E:ILE73 4.1 42.2 1.0 CG1 E:ILE73 4.1 43.5 1.0 C E:TRP72 4.2 47.8 1.0 CG2 E:VAL5 4.2 72.4 1.0 N E:TRP72 4.3 46.3 1.0 CD1 E:ILE73 4.3 53.4 1.0 C E:PRO68 4.3 61.8 1.0 CA E:ILE73 4.5 40.2 1.0 O E:ILE73 4.8 44.1 1.0 CA E:ILE71 4.9 52.2 1.0 O E:GLU69 4.9 66.9 1.0 N E:ILE71 4.9 54.2 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