Sodium in PDB 6hzw: The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution

The structure of The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution, PDB code: 6hzw 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)	20.00 / 2.22
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.416, 133.401, 160.474, 90.00, 102.48, 90.00
R / Rfree (%)	19.5 / 22

The structure of The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution (pdb code 6hzw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution, PDB code: 6hzw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:59.6 occ:1.00 O A:ILE71 2.3 46.8 1.0 O A:PRO68 2.8 61.2 1.0 C A:ILE71 3.5 38.5 1.0 N A:ILE73 3.8 41.3 1.0 C A:PRO68 3.9 60.3 1.0 CA A:TRP72 4.0 39.5 1.0 CG1 A:ILE73 4.1 40.9 1.0 N A:TRP72 4.2 37.1 1.0 C A:TRP72 4.3 41.2 1.0 CB A:ILE73 4.3 35.1 1.0 O A:GLU69 4.4 65.3 1.0 CA A:GLU69 4.4 66.1 1.0 C A:GLU69 4.6 62.1 1.0 N A:GLU69 4.6 63.8 1.0 N A:ILE71 4.7 49.4 1.0 CA A:ILE71 4.7 45.4 1.0 CD1 A:ILE73 4.7 46.4 1.0 CA A:ILE73 4.7 32.9 1.0

Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:53.9 occ:1.00 O B:ILE71 2.3 43.5 1.0 O B:PRO68 2.6 56.5 1.0 C B:ILE71 3.5 35.7 1.0 C B:PRO68 3.8 47.0 1.0 N B:ILE73 3.9 32.9 1.0 CG1 B:ILE73 4.1 36.7 1.0 CA B:TRP72 4.2 30.7 1.0 CA B:GLU69 4.3 57.1 1.0 CB B:ILE73 4.3 34.5 1.0 N B:TRP72 4.3 30.0 1.0 O B:GLU69 4.3 60.2 1.0 C B:TRP72 4.3 31.2 1.0 C B:GLU69 4.4 53.0 1.0 N B:GLU69 4.5 53.0 1.0 N B:ILE71 4.6 40.2 1.0 CA B:ILE71 4.6 35.6 1.0 CD1 B:ILE73 4.7 42.4 1.0 CA B:ILE73 4.8 29.8 1.0 CA B:PRO68 4.9 47.8 1.0

Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:57.7 occ:1.00 O D:HOH544 3.6 53.9 1.0 OG1 C:THR226 3.6 40.0 1.0 O C:HOH549 3.9 50.0 1.0 OG1 D:THR226 4.0 35.0 1.0 OG1 B:THR226 4.3 26.9 1.0 OG1 E:THR226 4.6 36.3 1.0 O E:HOH513 4.7 47.9 1.0 CB C:THR226 4.8 31.2 1.0 OG1 A:THR226 4.8 32.0 1.0 O B:HOH549 4.8 44.6 1.0 CG2 C:THR226 4.8 31.0 1.0

Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na407 b:54.0 occ:1.00 O C:ILE71 2.3 48.0 1.0 O C:PRO68 2.8 57.7 1.0 C C:ILE71 3.5 38.2 1.0 N C:ILE73 3.8 38.7 1.0 CG1 C:ILE73 4.0 33.5 1.0 CA C:TRP72 4.0 39.4 1.0 C C:PRO68 4.0 53.1 1.0 N C:TRP72 4.2 33.5 1.0 C C:TRP72 4.2 40.5 1.0 CB C:ILE73 4.2 30.8 1.0 O C:GLU69 4.5 53.2 1.0 CA C:GLU69 4.5 54.8 1.0 CD1 C:ILE73 4.6 38.4 1.0 C C:GLU69 4.7 51.3 1.0 CA C:ILE73 4.7 30.0 1.0 N C:ILE71 4.7 46.1 1.0 CA C:ILE71 4.7 40.3 1.0 N C:GLU69 4.7 48.3 1.0

Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:62.7 occ:1.00 O D:ILE71 2.3 49.7 1.0 O D:PRO68 3.0 62.2 1.0 C D:ILE71 3.5 44.9 1.0 N D:ILE73 3.7 38.4 1.0 CA D:TRP72 3.8 46.6 1.0 N D:TRP72 4.1 41.7 1.0 C D:TRP72 4.1 41.0 1.0 CG1 D:ILE73 4.1 34.1 1.0 C D:PRO68 4.2 59.4 1.0 CB D:ILE73 4.3 34.8 1.0 O D:GLU69 4.5 60.7 1.0 CA D:GLU69 4.6 58.0 1.0 CA D:ILE73 4.6 35.6 1.0 CA D:ILE71 4.7 45.8 1.0 N D:ILE71 4.7 50.3 1.0 C D:GLU69 4.7 55.3 1.0 N D:GLU69 4.9 61.2 1.0 CD1 D:ILE73 4.9 37.9 1.0

Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Glic Pentameric Ligand-Gated Ion Channel 2.22 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Na406 b:55.8 occ:1.00 O E:ILE71 2.3 53.0 1.0 O E:PRO68 2.3 60.1 1.0 C E:PRO68 3.4 63.1 1.0 C E:ILE71 3.5 42.4 1.0 CA E:GLU69 3.9 68.9 1.0 CG1 E:ILE73 4.0 35.4 1.0 O E:GLU69 4.1 66.8 1.0 N E:GLU69 4.1 70.4 1.0 C E:GLU69 4.1 61.9 1.0 N E:ILE73 4.2 41.1 1.0 CA E:TRP72 4.3 38.4 1.0 N E:TRP72 4.3 34.8 1.0 N E:ILE71 4.4 52.3 1.0 CB E:ILE73 4.4 33.1 1.0 C E:TRP72 4.5 39.6 1.0 CD1 E:ILE73 4.5 40.5 1.0 CA E:ILE71 4.5 45.2 1.0 CA E:PRO68 4.6 61.6 1.0 N E:ALA70 4.9 59.1 1.0 CA E:ILE73 5.0 31.9 1.0

H.Hu, K.Ataka, A.Menny, Z.Fourati, L.Sauguet, P.J.Corringer, P.Koehl, J.Heberle, M.Delarue. Electrostatics, Proton Sensor, and Networks Governing the Gating Transition in Glic, A Proton-Gated Pentameric Ion Channel. Proc. Natl. Acad. Sci. V. 115 12172 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30541892
DOI: 10.1073/PNAS.1813378116