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Sodium in PDB 6hy5: The Glic Pentameric Ligand-Gated Ion Channel Mutant Q193C

Protein crystallography data

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant Q193C, PDB code: 6hy5 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 / 2.58
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 182.420, 133.490, 161.010, 90.00, 102.18, 90.00
R / Rfree (%) 19.9 / 20.5

Other elements in 6hy5:

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant Q193C also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Q193C (pdb code 6hy5). 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 Q193C, PDB code: 6hy5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6hy5

Go back to Sodium Binding Sites List in 6hy5
Sodium binding site 1 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Q193C


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 Q193C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:69.6
occ:1.00
O A:ILE71 2.7 68.8 1.0
N A:ILE73 3.4 57.9 1.0
O A:PRO68 3.4 80.8 1.0
C A:ILE71 3.8 70.8 1.0
CA A:TRP72 3.9 62.9 1.0
CB A:ILE73 3.9 57.5 1.0
C A:TRP72 4.0 65.7 1.0
CA A:ILE73 4.2 55.2 1.0
CG1 A:VAL5 4.3 83.1 1.0
CG1 A:ILE73 4.3 58.8 1.0
N A:TRP72 4.3 65.2 1.0
CD1 A:ILE73 4.4 67.1 1.0
O A:ILE73 4.4 54.5 1.0
C A:PRO68 4.5 81.2 1.0
C A:ILE73 4.9 54.4 1.0

Sodium binding site 2 out of 6 in 6hy5

Go back to Sodium Binding Sites List in 6hy5
Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Q193C


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 Q193C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:70.6
occ:1.00
O B:ILE71 2.7 55.1 1.0
O B:PRO68 3.4 67.3 1.0
N B:ILE73 3.6 48.0 1.0
C B:ILE71 3.8 56.0 1.0
CA B:TRP72 4.0 48.0 1.0
CG1 B:VAL5 4.1 88.2 1.0
C B:TRP72 4.2 52.6 1.0
CB B:ILE73 4.3 47.9 1.0
CD1 B:ILE73 4.3 56.9 1.0
N B:TRP72 4.4 49.9 1.0
C B:PRO68 4.5 67.5 1.0
CA B:ILE73 4.5 45.5 1.0
O B:ILE73 4.7 48.7 1.0
CG1 B:ILE73 4.8 49.4 1.0
O B:GLU69 4.8 69.9 1.0
CA B:GLU69 4.8 65.1 1.0

Sodium binding site 3 out of 6 in 6hy5

Go back to Sodium Binding Sites List in 6hy5
Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Q193C


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 Q193C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:62.6
occ:1.00
OG1 D:THR226 3.7 49.7 1.0
OG1 C:THR226 4.0 49.3 1.0
OG1 E:THR226 4.2 48.1 1.0
CG2 D:THR226 4.5 41.8 1.0
CG2 C:THR226 4.5 45.0 1.0
CB D:THR226 4.7 45.2 1.0
OG1 B:THR226 4.8 40.8 1.0
OG1 A:THR226 4.9 47.5 1.0
CB C:THR226 4.9 48.4 1.0
O A:HOH517 5.0 42.5 1.0

Sodium binding site 4 out of 6 in 6hy5

Go back to Sodium Binding Sites List in 6hy5
Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Q193C


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 Q193C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na406

b:75.8
occ:1.00
O C:ILE71 2.7 68.6 1.0
O C:PRO68 3.4 74.1 1.0
N C:ILE73 3.6 56.7 1.0
C C:ILE71 3.9 69.3 1.0
CA C:TRP72 4.0 60.5 1.0
CG1 C:VAL5 4.2 89.2 1.0
CB C:ILE73 4.2 55.2 1.0
C C:TRP72 4.2 62.6 1.0
N C:TRP72 4.4 62.8 1.0
C C:PRO68 4.4 73.9 1.0
CG1 C:ILE73 4.5 55.4 1.0
CA C:ILE73 4.5 53.9 1.0
CD1 C:ILE73 4.5 61.1 1.0
O C:ILE73 4.7 60.0 1.0
CA C:GLU69 4.9 72.0 1.0
O C:GLU69 4.9 75.7 1.0

Sodium binding site 5 out of 6 in 6hy5

Go back to Sodium Binding Sites List in 6hy5
Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Q193C


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 Q193C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na405

b:89.2
occ:1.00
O D:ILE71 2.7 72.9 1.0
O D:PRO68 3.4 78.5 1.0
N D:ILE73 3.6 60.7 1.0
C D:ILE71 3.8 75.3 1.0
CA D:TRP72 4.0 68.0 1.0
CG1 D:VAL5 4.1 99.5 1.0
CB D:ILE73 4.2 59.0 1.0
C D:TRP72 4.2 69.2 1.0
N D:TRP72 4.4 70.6 1.0
CA D:ILE73 4.5 57.3 1.0
C D:PRO68 4.5 78.6 1.0
CG1 D:ILE73 4.5 59.5 1.0
CD1 D:ILE73 4.5 67.2 1.0
O D:ILE73 4.7 58.8 1.0
CA D:GLU69 4.8 75.8 1.0
O D:GLU69 4.9 80.6 1.0

Sodium binding site 6 out of 6 in 6hy5

Go back to Sodium Binding Sites List in 6hy5
Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Q193C


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 Q193C within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na405

b:85.4
occ:1.00
O E:ILE71 2.7 66.6 1.0
O E:PRO68 3.3 75.2 1.0
N E:ILE73 3.6 57.0 1.0
C E:ILE71 3.9 68.2 1.0
CA E:TRP72 4.0 61.5 1.0
CG1 E:VAL5 4.1 90.4 1.0
CB E:ILE73 4.2 56.2 1.0
C E:TRP72 4.2 63.3 1.0
N E:TRP72 4.4 63.3 1.0
C E:PRO68 4.4 75.9 1.0
CG1 E:ILE73 4.5 57.3 1.0
CA E:ILE73 4.5 54.0 1.0
CD1 E:ILE73 4.5 69.6 1.0
O E:ILE73 4.7 56.2 1.0
CA E:GLU69 4.9 74.2 1.0
O E:GLU69 4.9 77.1 1.0

Reference:

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
Page generated: Tue Dec 15 12:22:19 2020

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