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

Protein crystallography data

The structure of The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant Complexed to Bromoform, PDB code: 4hfd 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) 27.73 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.218, 132.869, 159.376, 90.00, 102.29, 90.00
R / Rfree (%) 19.5 / 20.8

Other elements in 4hfd:

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

Bromine (Br) 60 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 Bromoform (pdb code 4hfd). 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 Bromoform, PDB code: 4hfd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4hfd

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


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

b:82.1
occ:1.00
 O A:ILE71 2.6 84.5 1.0
O A:PRO68 3.2 96.5 1.0
N A:ILE73 3.6 76.4 1.0
C A:ILE71 3.7 84.9 1.0
CA A:TRP72 4.0 79.2 1.0
C A:TRP72 4.2 84.0 1.0
CB A:ILE73 4.2 75.1 1.0
N A:TRP72 4.3 80.1 1.0
C A:PRO68 4.3 96.2 1.0
CG1 A:ILE73 4.4 75.5 1.0
CD1 A:ILE73 4.4 83.3 1.0
CA A:ILE73 4.5 74.0 1.0
O A:GLU69 4.7 91.4 1.0
CA A:GLU69 4.7 90.5 1.0
CG1 A:VAL5 4.8 0.9 1.0
O A:ILE73 4.8 78.3 1.0
C A:GLU69 4.9 91.6 1.0
CA A:ILE71 4.9 83.2 1.0
N A:GLU69 4.9 91.4 1.0
N A:ILE71 5.0 84.6 1.0

Sodium binding site 2 out of 6 in 4hfd

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


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 Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:77.3
occ:1.00
 O B:ILE71 2.5 75.0 1.0
O B:PRO68 2.8 86.9 1.0
C B:ILE71 3.7 74.2 1.0
N B:ILE73 3.8 68.0 1.0
C B:PRO68 3.9 87.1 1.0
CD1 B:ILE73 4.0 79.4 1.0
CA B:TRP72 4.2 69.1 1.0
CB B:ILE73 4.3 68.1 1.0
C B:TRP72 4.3 73.5 1.0
CA B:GLU69 4.3 84.1 1.0
O B:GLU69 4.4 85.3 1.0
N B:TRP72 4.4 69.9 1.0
C B:GLU69 4.5 83.8 1.0
N B:GLU69 4.6 84.0 1.0
CG1 B:ILE73 4.6 68.5 1.0
CA B:ILE73 4.6 65.9 1.0
N B:ILE71 4.8 72.2 1.0
CA B:ILE71 4.8 70.4 1.0
CG1 B:VAL5 4.9 0.2 1.0

Sodium binding site 3 out of 6 in 4hfd

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


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 Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:90.5
occ:1.00
 OG1 C:THR226 3.7 86.0 1.0
OG1 D:THR226 4.1 83.7 1.0
OG1 B:THR226 4.2 84.7 1.0
OG1 E:THR226 4.6 88.0 1.0
OG1 A:THR226 4.6 87.8 1.0
CG2 C:THR226 4.6 82.2 1.0
CB C:THR226 4.8 85.5 1.0
CG2 B:THR226 4.9 76.0 1.0

Sodium binding site 4 out of 6 in 4hfd

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


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

b:78.1
occ:1.00
 O C:ILE71 2.5 85.4 1.0
O C:PRO68 3.0 91.2 1.0
C C:ILE71 3.7 85.3 1.0
N C:ILE73 3.7 73.7 1.0
C C:PRO68 4.0 90.2 1.0
CA C:TRP72 4.1 76.1 1.0
CB C:ILE73 4.1 72.6 1.0
CD1 C:ILE73 4.1 81.5 1.0
CG1 C:ILE73 4.2 73.2 1.0
C C:TRP72 4.2 80.7 1.0
N C:TRP72 4.3 77.8 1.0
CA C:GLU69 4.5 87.3 1.0
CA C:ILE73 4.5 70.8 1.0
O C:GLU69 4.6 90.2 1.0
N C:GLU69 4.7 86.9 1.0
C C:GLU69 4.7 90.6 1.0
CG1 C:VAL5 4.8 0.3 1.0
N C:ILE71 4.9 86.2 1.0
CA C:ILE71 4.9 85.0 1.0

Sodium binding site 5 out of 6 in 4hfd

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


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 Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:91.0
occ:1.00
 O D:ILE71 2.7 87.3 1.0
O D:PRO68 3.2 96.7 1.0
C D:ILE71 3.9 87.7 1.0
N D:ILE73 3.9 78.3 1.0
CG2 D:VAL5 4.0 1.0 1.0
CA D:TRP72 4.2 80.5 1.0
C D:PRO68 4.3 97.8 1.0
CB D:ILE73 4.4 77.8 1.0
C D:TRP72 4.4 85.2 1.0
N D:TRP72 4.5 82.2 1.0
O D:GLU69 4.5 95.9 1.0
CA D:GLU69 4.6 94.1 1.0
CD1 D:ILE73 4.6 85.0 1.0
CG1 D:ILE73 4.6 78.1 1.0
CA D:ILE73 4.7 76.0 1.0
C D:GLU69 4.8 95.7 1.0
N D:GLU69 4.8 94.7 1.0
O D:ILE73 5.0 78.9 1.0

Sodium binding site 6 out of 6 in 4hfd

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


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 Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na403

b:78.3
occ:1.00
 O E:ILE71 2.7 86.6 1.0
O E:PRO68 2.9 93.6 1.0
C E:ILE71 3.9 86.9 1.0
C E:PRO68 3.9 94.6 1.0
N E:ILE73 4.0 75.6 1.0
CD1 E:ILE73 4.2 78.5 1.0
CB E:ILE73 4.3 76.2 1.0
CG1 E:ILE73 4.4 75.7 1.0
CA E:TRP72 4.4 78.8 1.0
CA E:GLU69 4.4 93.2 1.0
O E:GLU69 4.5 97.0 1.0
C E:TRP72 4.5 81.7 1.0
N E:GLU69 4.5 93.2 1.0
N E:TRP72 4.6 80.2 1.0
C E:GLU69 4.7 96.1 1.0
CA E:ILE73 4.8 73.7 1.0
CG1 E:VAL5 4.9 0.3 1.0
N E:ILE71 5.0 88.6 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 15:48:40 2024

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