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Sodium in PDB 4hfc: The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol

Protein crystallography data

The structure of The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol, PDB code: 4hfc was solved by L.Sauguet, R.J.Howard, L.Malherbe, U.S.Lee, P.J.Corringer, R.A.Harris, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 180.880, 133.140, 159.350, 90.00, 102.22, 90.00
R / Rfree (%) 19.2 / 22

Other elements in 4hfc:

The structure of The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol also contains other interesting chemical elements:

Bromine (Br) 5 atoms
Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol (pdb code 4hfc). 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 F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol, PDB code: 4hfc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4hfc

Go back to Sodium Binding Sites List in 4hfc
Sodium binding site 1 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol


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 F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:89.1
occ:1.00
 OG1 C:THR226 4.1 94.5 1.0
OG1 B:THR226 4.1 89.6 1.0
OG1 A:THR226 4.2 93.4 1.0
OG1 E:THR226 4.5 88.4 1.0
OG1 D:THR226 4.7 88.8 1.0
CG2 B:THR226 4.8 81.5 1.0
CG2 C:THR226 4.9 83.7 1.0
CG2 A:THR226 4.9 83.5 1.0
O A:HOH516 4.9 55.0 1.0

Sodium binding site 2 out of 6 in 4hfc

Go back to Sodium Binding Sites List in 4hfc
Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol


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 F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:86.1
occ:1.00
 O A:ILE71 2.6 91.4 1.0
O A:PRO68 3.2 0.2 1.0
C A:ILE71 3.6 92.6 1.0
N A:ILE73 3.8 82.4 1.0
CA A:TRP72 4.0 86.0 1.0
CG1 A:VAL5 4.1 0.2 1.0
N A:TRP72 4.2 87.7 1.0
C A:PRO68 4.2 0.9 1.0
C A:TRP72 4.3 89.4 1.0
CD1 A:ILE73 4.3 88.7 1.0
CG1 A:ILE73 4.3 82.4 1.0
CB A:ILE73 4.5 81.5 1.0
O A:GLU69 4.5 0.9 1.0
CA A:ILE73 4.7 80.0 1.0
C A:GLU69 4.8 0.5 1.0
CA A:GLU69 4.8 0.7 1.0
CA A:ILE71 4.8 92.4 1.0
N A:ILE71 4.8 94.5 1.0
CB A:VAL5 4.9 0.1 1.0
N A:GLU69 4.9 0.6 1.0

Sodium binding site 3 out of 6 in 4hfc

Go back to Sodium Binding Sites List in 4hfc
Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol


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 F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:84.2
occ:1.00
 O B:ILE71 2.6 84.8 1.0
O B:PRO68 3.0 93.1 1.0
C B:ILE71 3.7 83.2 1.0
C B:PRO68 4.0 92.5 1.0
N B:ILE73 4.1 74.6 1.0
CG1 B:VAL5 4.1 0.7 1.0
O B:GLU69 4.2 93.2 1.0
CA B:TRP72 4.2 77.6 1.0
N B:TRP72 4.4 78.1 1.0
CD1 B:ILE73 4.4 81.9 1.0
C B:GLU69 4.4 91.9 1.0
CA B:GLU69 4.5 90.4 1.0
C B:TRP72 4.5 80.2 1.0
CG1 B:ILE73 4.6 72.6 1.0
N B:GLU69 4.6 90.3 1.0
N B:ILE71 4.7 80.3 1.0
CB B:ILE73 4.7 72.8 1.0
CA B:ILE71 4.8 78.7 1.0
CB B:VAL5 4.9 0.3 1.0
CA B:ILE73 5.0 71.7 1.0

Sodium binding site 4 out of 6 in 4hfc

Go back to Sodium Binding Sites List in 4hfc
Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol


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 F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na405

b:76.3
occ:1.00
 O C:ILE71 2.8 89.1 1.0
O C:PRO68 3.3 90.1 1.0
N C:ILE73 3.5 80.4 1.0
C C:ILE71 3.9 91.2 1.0
CB C:ILE73 4.0 79.1 1.0
CD1 C:ILE73 4.0 82.1 1.0
CG1 C:ILE73 4.1 79.5 1.0
CA C:TRP72 4.1 83.6 1.0
C C:TRP72 4.2 86.7 1.0
CA C:ILE73 4.3 77.8 1.0
C C:PRO68 4.4 91.5 1.0
N C:TRP72 4.5 85.0 1.0
O C:ILE73 4.6 85.5 1.0
CG1 C:VAL5 4.7 0.4 1.0
C C:ILE73 5.0 85.2 1.0

Sodium binding site 5 out of 6 in 4hfc

Go back to Sodium Binding Sites List in 4hfc
Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol


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 F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na405

b:96.0
occ:1.00
 O D:ILE71 2.6 90.7 1.0
O D:PRO68 3.2 0.0 1.0
N D:ILE73 3.5 82.4 1.0
C D:ILE71 3.7 92.2 1.0
CA D:TRP72 4.0 85.7 1.0
CD1 D:ILE73 4.1 91.9 1.0
C D:TRP72 4.1 87.7 1.0
CG1 D:ILE73 4.1 83.3 1.0
CB D:ILE73 4.2 82.5 1.0
C D:PRO68 4.2 0.4 1.0
N D:TRP72 4.2 87.2 1.0
CA D:ILE73 4.4 80.6 1.0
O D:ILE73 4.7 87.4 1.0
O D:GLU69 4.8 0.8 1.0
CA D:GLU69 4.9 99.3 1.0
CA D:ILE71 4.9 92.0 1.0
N D:GLU69 5.0 0.5 1.0
N D:ILE71 5.0 94.7 1.0
C D:GLU69 5.0 0.8 1.0

Sodium binding site 6 out of 6 in 4hfc

Go back to Sodium Binding Sites List in 4hfc
Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol


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 F14'A Ethanol-Sensitive Mutant Complexed to 2-Bromo-Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na406

b:97.0
occ:1.00
 O E:ILE71 2.7 92.3 1.0
O E:PRO68 2.8 99.9 1.0
C E:PRO68 3.8 0.7 1.0
C E:ILE71 3.8 93.3 1.0
CD1 E:ILE73 3.8 82.5 1.0
N E:ILE73 3.9 78.5 1.0
CG1 E:ILE73 4.1 78.4 1.0
CB E:ILE73 4.2 77.7 1.0
CA E:TRP72 4.4 85.3 1.0
C E:TRP72 4.5 84.8 1.0
N E:GLU69 4.5 99.8 1.0
CA E:GLU69 4.5 99.8 1.0
N E:TRP72 4.5 87.6 1.0
O E:GLU69 4.5 0.7 1.0
CG1 E:VAL5 4.7 0.1 1.0
C E:GLU69 4.7 0.5 1.0
CA E:ILE73 4.7 75.4 1.0
CA E:PRO68 4.8 93.2 1.0
N E:ILE71 4.9 92.8 1.0
CA E:ILE71 5.0 91.2 1.0

Reference:

L.Sauguet, R.J.Howard, L.Malherbe, U.S.Lee, P.J.Corringer, R.A.Harris, M.Delarue. Structural Basis For Potentiation By Alcohols and Anaesthetics in A Ligand-Gated Ion Channel. Nat Commun V. 4 1697 2013.
ISSN: ESSN 2041-1723
PubMed: 23591864
DOI: 10.1038/NCOMMS2682
Page generated: Mon Oct 7 15:47:10 2024

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