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

Protein crystallography data

The structure of The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to Ethanol, PDB code: 4hfe 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 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 180.990, 133.620, 159.130, 90.00, 102.17, 90.00
R / Rfree (%) 20.5 / 21.5

Other elements in 4hfe:

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

Sodium binding site 1 out of 6 in 4hfe

Go back to Sodium Binding Sites List in 4hfe
Sodium binding site 1 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 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 Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:86.7
occ:1.00
 O A:ILE71 2.7 0.9 1.0
N A:ILE73 3.4 93.2 1.0
O A:PRO68 3.5 0.5 1.0
C A:ILE71 3.7 0.8 1.0
CA A:TRP72 3.8 98.8 1.0
C A:TRP72 3.9 0.6 1.0
CG2 A:VAL5 4.0 0.5 1.0
CB A:ILE73 4.0 91.9 1.0
N A:TRP72 4.2 0.7 1.0
CA A:ILE73 4.2 90.3 1.0
CG1 A:ILE73 4.3 93.2 1.0
CD1 A:ILE73 4.4 98.2 1.0
O A:ILE73 4.5 91.2 1.0
C A:PRO68 4.6 0.1 1.0
C A:ILE73 4.9 91.8 1.0

Sodium binding site 2 out of 6 in 4hfe

Go back to Sodium Binding Sites List in 4hfe
Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 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 Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:96.7
occ:1.00
 OG1 C:THR226 4.2 74.4 1.0
OG1 D:THR226 4.2 74.6 1.0
OG1 E:THR226 4.3 80.5 1.0
OG1 B:THR226 4.3 76.9 1.0
OG1 A:THR226 4.4 76.5 1.0

Sodium binding site 3 out of 6 in 4hfe

Go back to Sodium Binding Sites List in 4hfe
Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 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 Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:76.2
occ:1.00
 O B:ILE71 2.5 87.2 1.0
O B:PRO68 3.2 96.0 1.0
N B:ILE73 3.4 80.6 1.0
C B:ILE71 3.6 87.0 1.0
CA B:TRP72 3.8 82.6 1.0
C B:TRP72 4.0 85.8 1.0
CG2 B:VAL5 4.1 0.4 1.0
CB B:ILE73 4.1 80.9 1.0
CD1 B:ILE73 4.1 94.1 1.0
N B:TRP72 4.1 83.2 1.0
CA B:ILE73 4.3 78.5 1.0
C B:PRO68 4.3 97.0 1.0
CG1 B:ILE73 4.5 82.5 1.0
O B:ILE73 4.7 81.3 1.0
O B:GLU69 4.8 99.3 1.0
CA B:GLU69 4.8 96.7 1.0
CA B:ILE71 4.8 83.2 1.0
N B:ILE71 4.9 85.1 1.0
C B:GLU69 5.0 98.3 1.0
N B:GLU69 5.0 95.5 1.0

Sodium binding site 4 out of 6 in 4hfe

Go back to Sodium Binding Sites List in 4hfe
Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 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 Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:79.3
occ:1.00
 O C:ILE71 2.7 97.7 1.0
O C:PRO68 3.2 0.5 1.0
N C:ILE73 3.8 90.6 1.0
C C:ILE71 3.8 98.9 1.0
CA C:TRP72 4.1 92.9 1.0
CG2 C:VAL5 4.1 0.3 1.0
CB C:ILE73 4.2 89.8 1.0
C C:PRO68 4.3 0.8 1.0
C C:TRP72 4.3 96.8 1.0
CG1 C:ILE73 4.4 90.6 1.0
CD1 C:ILE73 4.4 97.6 1.0
N C:TRP72 4.4 94.5 1.0
CA C:ILE73 4.6 87.7 1.0
CA C:GLU69 4.7 0.5 1.0
O C:GLU69 4.7 0.8 1.0
N C:GLU69 4.9 99.9 1.0
C C:GLU69 4.9 0.1 1.0
O C:ILE73 4.9 90.3 1.0

Sodium binding site 5 out of 6 in 4hfe

Go back to Sodium Binding Sites List in 4hfe
Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 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 Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na405

b:0.8
occ:1.00
 O D:ILE71 2.8 1.0 1.0
CG2 D:VAL5 3.4 0.4 1.0
N D:ILE73 3.6 94.1 1.0
CA D:TRP72 3.8 99.3 1.0
C D:ILE71 3.8 0.7 1.0
O D:PRO68 3.9 0.9 1.0
C D:TRP72 4.1 0.4 1.0
N D:TRP72 4.2 0.0 1.0
CB D:ILE73 4.5 93.7 1.0
CB D:VAL5 4.6 0.8 1.0
CA D:ILE73 4.6 91.2 1.0
O D:ILE73 4.6 91.6 1.0
CG1 D:ILE73 4.9 95.6 1.0
CB D:TRP72 4.9 98.3 1.0
O D:GLU69 5.0 0.1 1.0

Sodium binding site 6 out of 6 in 4hfe

Go back to Sodium Binding Sites List in 4hfe
Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to 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 Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na403

b:89.5
occ:1.00
 O E:PRO68 2.7 1.0 1.0
O E:ILE71 2.8 0.5 1.0
C E:PRO68 3.8 0.8 1.0
C E:ILE71 4.0 0.3 1.0
N E:ILE73 4.0 96.1 1.0
CD1 E:ILE73 4.1 0.2 1.0
CB E:ILE73 4.2 95.8 1.0
CG1 E:ILE73 4.3 96.9 1.0
CA E:GLU69 4.3 0.6 1.0
N E:GLU69 4.4 0.7 1.0
CA E:TRP72 4.5 0.6 1.0
C E:TRP72 4.6 0.2 1.0
O E:GLU69 4.6 0.8 1.0
C E:GLU69 4.6 0.5 1.0
N E:TRP72 4.7 0.0 1.0
CA E:ILE73 4.7 93.4 1.0
CA E:PRO68 4.8 0.9 1.0
CG2 E:VAL5 4.9 0.9 1.0
N E:ILE71 5.0 0.8 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 15:48:41 2024

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