Sodium in PDB 6hz0: The Glic Pentameric Ligand-Gated Ion Channel Mutant K248A

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant K248A, PDB code: 6hz0 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 / 2.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.871, 132.678, 159.329, 90.00, 101.95, 90.00
R / Rfree (%)	21 / 23.8

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant K248A 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 Mutant K248A (pdb code 6hz0). 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 Mutant K248A, PDB code: 6hz0:
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 Mutant K248A


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 Mutant K248A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:79.3 occ:1.00 O A:ILE71 2.3 82.0 1.0 O A:PRO68 2.9 85.4 1.0 C A:ILE71 3.5 70.1 1.0 N A:ILE73 3.5 89.9 1.0 CG1 A:ILE73 3.7 77.3 1.0 CB A:ILE73 3.9 70.3 1.0 CA A:TRP72 3.9 78.8 1.0 C A:TRP72 4.0 86.5 1.0 C A:PRO68 4.1 0.5 1.0 N A:TRP72 4.1 71.9 1.0 CA A:ILE73 4.3 81.6 1.0 CD1 A:ILE73 4.5 85.7 1.0 O A:GLU69 4.5 0.6 1.0 CA A:GLU69 4.6 0.1 1.0 CA A:ILE71 4.7 82.4 1.0 O A:ILE73 4.7 77.3 1.0 C A:GLU69 4.7 0.1 1.0 N A:ILE71 4.8 90.8 1.0 N A:GLU69 4.8 0.2 1.0

Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant K248A


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 Mutant K248A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:58.7 occ:1.00 O B:HOH557 3.5 64.7 1.0 O E:HOH546 3.9 58.4 1.0 OG1 A:THR226 4.0 50.5 1.0 OG1 E:THR226 4.2 46.1 1.0 OG1 B:THR226 4.2 57.7 1.0 OG1 C:THR226 4.3 56.0 1.0 OG1 D:THR226 4.4 52.5 1.0

Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant K248A


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 Mutant K248A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:65.4 occ:1.00 O B:ILE71 2.3 85.5 1.0 O B:PRO68 2.6 80.2 1.0 C B:ILE71 3.5 71.7 1.0 C B:PRO68 3.8 83.3 1.0 N B:ILE73 3.9 76.5 1.0 CG1 B:ILE73 4.0 70.1 1.0 O B:GLU69 4.1 99.5 1.0 CA B:GLU69 4.1 0.2 1.0 CA B:TRP72 4.2 74.2 1.0 CB B:ILE73 4.2 67.2 1.0 N B:TRP72 4.3 73.6 1.0 C B:GLU69 4.3 95.8 1.0 C B:TRP72 4.4 81.9 1.0 N B:GLU69 4.4 90.1 1.0 N B:ILE71 4.6 86.2 1.0 CA B:ILE71 4.6 73.8 1.0 CA B:ILE73 4.7 64.5 1.0 CD1 B:ILE73 4.7 78.7 1.0 CA B:PRO68 4.9 83.8 1.0

Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant K248A


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 Mutant K248A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na406 b:79.2 occ:1.00 O C:ILE71 2.3 92.7 1.0 O C:PRO68 2.8 94.9 1.0 C C:ILE71 3.5 83.1 1.0 N C:ILE73 3.9 89.2 1.0 C C:PRO68 4.0 0.6 1.0 CA C:TRP72 4.1 80.9 1.0 CG1 C:ILE73 4.1 81.6 1.0 O C:GLU69 4.2 0.2 1.0 N C:TRP72 4.2 76.5 1.0 CA C:GLU69 4.3 0.1 1.0 CB C:ILE73 4.3 71.9 1.0 C C:TRP72 4.3 85.7 1.0 C C:GLU69 4.4 0.8 1.0 N C:GLU69 4.6 0.8 1.0 N C:ILE71 4.6 90.5 1.0 CA C:ILE71 4.6 89.7 1.0 CA C:ILE73 4.7 77.9 1.0 CD1 C:ILE73 4.8 92.4 1.0

Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant K248A


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 Mutant K248A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:80.3 occ:1.00 O D:ILE71 2.3 90.1 1.0 O D:PRO68 2.8 81.3 1.0 C D:ILE71 3.5 81.5 1.0 N D:ILE73 3.9 92.8 1.0 C D:PRO68 3.9 95.0 1.0 CA D:TRP72 4.1 90.9 1.0 CG1 D:ILE73 4.1 73.7 1.0 O D:GLU69 4.1 0.3 1.0 CA D:GLU69 4.2 0.5 1.0 N D:TRP72 4.3 82.1 1.0 CB D:ILE73 4.3 72.3 1.0 C D:TRP72 4.3 97.3 1.0 C D:GLU69 4.4 0.3 1.0 N D:GLU69 4.6 0.9 1.0 N D:ILE71 4.6 0.6 1.0 CA D:ILE71 4.7 91.3 1.0 CA D:ILE73 4.7 81.7 1.0 CD1 D:ILE73 4.8 77.9 1.0

Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant K248A


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 Mutant K248A within 5.0Å range: probe atom residue distance (Å) B Occ E:Na407 b:86.8 occ:1.00 O E:ILE71 2.2 82.0 1.0 O E:PRO68 2.3 0.7 1.0 C E:PRO68 3.4 0.1 1.0 C E:ILE71 3.5 80.2 1.0 CA E:GLU69 3.9 0.1 1.0 O E:GLU69 4.0 0.3 1.0 CG1 E:ILE73 4.0 79.1 1.0 C E:GLU69 4.1 0.9 1.0 N E:GLU69 4.1 0.2 1.0 N E:ILE73 4.1 93.7 1.0 CB E:ILE73 4.3 78.7 1.0 CA E:TRP72 4.3 81.9 1.0 N E:TRP72 4.3 80.8 1.0 N E:ILE71 4.4 97.1 1.0 C E:TRP72 4.5 87.6 1.0 CD1 E:ILE73 4.5 82.7 1.0 CA E:ILE71 4.5 88.2 1.0 CA E:PRO68 4.6 0.2 1.0 CA E:ILE73 4.9 79.5 1.0 N E:ALA70 4.9 0.3 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