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Sodium in PDB 6i08: The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W

Protein crystallography data

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W, PDB code: 6i08 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 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 180.800, 134.350, 159.350, 90.00, 101.83, 90.00
R / Rfree (%) 20.9 / 22.8

Other elements in 6i08:

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W (pdb code 6i08). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W, PDB code: 6i08:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 6i08

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Sodium binding site 1 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W


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 E243C-I201W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na404

b:87.8
occ:1.00
 O D:PRO74 3.4 97.8 1.0
O D:ILE76 3.5 94.2 1.0
N D:ILE76 3.6 90.2 1.0
NH1 D:ARG77 4.0 0.4 1.0
CB D:ILE76 4.2 93.3 1.0
CA D:ILE76 4.2 90.0 1.0
C D:ILE76 4.3 93.5 1.0
CD1 D:LEU45 4.4 94.1 1.0
CA D:GLU75 4.5 90.9 1.0
OH D:TYR102 4.5 0.1 1.0
C D:GLU75 4.5 94.5 1.0
C D:PRO74 4.5 97.5 1.0
OE1 D:GLU104 4.5 0.7 1.0
CG2 D:ILE73 4.6 0.2 1.0
CG1 D:ILE76 4.6 94.6 1.0
CZ D:TYR102 4.9 0.6 1.0
N D:GLU75 5.0 92.2 1.0

Sodium binding site 2 out of 7 in 6i08

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Sodium binding site 2 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W


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 E243C-I201W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:80.5
occ:1.00
 OG B:SER230 4.7 92.2 1.0
OG A:SER230 4.9 91.0 1.0
OG C:SER230 5.0 97.2 1.0

Sodium binding site 3 out of 7 in 6i08

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Sodium binding site 3 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W


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 E243C-I201W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:1.0
occ:1.00
 OG1 A:THR226 3.7 94.2 1.0
OG1 E:THR226 4.0 99.6 1.0
OG1 B:THR226 4.1 0.0 1.0
CG2 E:THR226 4.5 93.2 1.0
OG1 C:THR226 4.5 0.8 1.0
OG1 D:THR226 4.5 98.2 1.0
CG2 A:THR226 4.6 82.9 1.0
CB A:THR226 4.7 89.1 1.0
CB E:THR226 4.9 96.0 1.0
CG2 B:THR226 5.0 94.8 1.0

Sodium binding site 4 out of 7 in 6i08

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Sodium binding site 4 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W


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 E243C-I201W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:75.1
occ:1.00
 O A:PRO74 3.7 96.7 1.0
O A:ILE76 3.7 87.9 1.0
NH1 A:ARG77 3.8 0.1 1.0
N A:ILE76 3.9 88.2 1.0
OH A:TYR102 4.3 0.3 1.0
OE1 A:GLU104 4.5 0.0 1.0
CB A:ILE76 4.5 89.9 1.0
CA A:ILE76 4.6 87.1 1.0
CG2 A:ILE73 4.6 94.6 1.0
C A:ILE76 4.6 87.6 1.0
CA A:GLU75 4.6 90.7 1.0
C A:GLU75 4.7 92.2 1.0
CD1 A:LEU45 4.8 85.6 1.0
C A:PRO74 4.8 95.8 1.0
CZ A:TYR102 4.8 99.7 1.0
CZ A:ARG77 5.0 0.6 1.0

Sodium binding site 5 out of 7 in 6i08

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Sodium binding site 5 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W


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 E243C-I201W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:78.9
occ:1.00
 O B:PRO74 3.3 85.5 1.0
O B:ILE76 3.7 86.2 1.0
N B:ILE76 3.8 77.2 1.0
NH1 B:ARG77 3.8 95.0 1.0
CG2 B:ILE73 4.3 79.6 1.0
C B:PRO74 4.4 84.3 1.0
CA B:GLU75 4.4 78.0 1.0
CA B:ILE76 4.5 77.9 1.0
OH B:TYR102 4.5 0.7 1.0
C B:GLU75 4.5 79.8 1.0
CB B:ILE76 4.6 80.4 1.0
C B:ILE76 4.6 85.4 1.0
CD1 B:LEU45 4.8 81.7 1.0
N B:GLU75 4.8 79.7 1.0
CG1 B:ILE76 4.9 81.8 1.0
OE1 B:GLU104 4.9 0.3 1.0
CZ B:TYR102 5.0 0.3 1.0

Sodium binding site 6 out of 7 in 6i08

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Sodium binding site 6 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W


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 E243C-I201W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:87.7
occ:1.00
 O C:PRO74 3.5 95.1 1.0
NH1 C:ARG77 3.7 0.1 1.0
N C:ILE76 3.8 91.0 1.0
O C:ILE76 3.8 94.5 1.0
CA C:GLU75 4.3 88.8 1.0
CG2 C:ILE73 4.5 90.6 1.0
OH C:TYR102 4.5 0.0 1.0
C C:PRO74 4.5 93.8 1.0
C C:GLU75 4.5 93.4 1.0
CA C:ILE76 4.7 91.3 1.0
C C:ILE76 4.7 94.0 1.0
OE1 C:GLU104 4.8 0.9 1.0
CB C:ILE76 4.8 95.4 1.0
N C:GLU75 4.9 89.4 1.0
CZ C:ARG77 4.9 0.6 1.0
CD1 C:LEU45 5.0 90.1 1.0
CZ C:TYR102 5.0 0.9 1.0

Sodium binding site 7 out of 7 in 6i08

Go back to Sodium Binding Sites List in 6i08
Sodium binding site 7 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C-I201W within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na403

b:78.8
occ:1.00
 O E:PRO74 3.5 0.2 1.0
O E:ILE76 3.8 0.1 1.0
N E:ILE76 3.9 97.0 1.0
NH1 E:ARG77 3.9 0.0 1.0
OH E:TYR102 4.3 0.7 1.0
CG2 E:ILE73 4.4 0.8 1.0
CB E:ILE76 4.5 99.2 1.0
CA E:ILE76 4.5 96.6 1.0
CD1 E:LEU45 4.6 88.4 1.0
C E:PRO74 4.6 0.7 1.0
CA E:GLU75 4.6 97.2 1.0
C E:ILE76 4.6 0.8 1.0
OE1 E:GLU104 4.7 92.1 1.0
C E:GLU75 4.7 99.9 1.0
CZ E:TYR102 4.8 0.3 1.0
CG1 E:ILE76 4.9 0.2 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 Oct 8 09:31:18 2024

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