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Sodium in PDB 4hfb: The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant (Apo)

Protein crystallography data

The structure of The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant (Apo), PDB code: 4hfb 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 / 2.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.737, 133.512, 161.120, 90.00, 103.28, 90.00
R / Rfree (%) 20.8 / 22.2

Other elements in 4hfb:

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

Sodium binding site 1 out of 6 in 4hfb

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


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

b:90.0
occ:1.00
 O A:ILE71 2.7 0.6 1.0
N A:ILE73 3.3 92.5 1.0
O A:PRO68 3.6 0.9 1.0
CA A:TRP72 3.7 98.2 1.0
C A:ILE71 3.8 0.9 1.0
C A:TRP72 3.9 0.4 1.0
CB A:ILE73 4.0 90.9 1.0
N A:TRP72 4.2 99.0 1.0
CA A:ILE73 4.2 89.3 1.0
CG1 A:ILE73 4.3 92.7 1.0
O A:ILE73 4.4 88.2 1.0
CD1 A:ILE73 4.5 0.6 1.0
CG1 A:VAL5 4.7 0.6 1.0
C A:PRO68 4.7 0.7 1.0
C A:ILE73 4.8 89.7 1.0
CB A:TRP72 5.0 97.9 1.0
O A:TRP72 5.0 0.7 1.0

Sodium binding site 2 out of 6 in 4hfb

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Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel F14'A Ethanol-Sensitive Mutant (Apo)


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

b:96.0
occ:1.00
 O B:ILE71 2.9 89.2 1.0
N B:ILE73 3.1 79.8 1.0
CA B:TRP72 3.7 81.4 1.0
C B:TRP72 3.8 86.1 1.0
O B:PRO68 3.9 92.7 1.0
C B:ILE71 3.9 88.1 1.0
CB B:ILE73 4.0 78.7 1.0
CA B:ILE73 4.0 76.9 1.0
O B:ILE73 4.1 78.7 1.0
N B:TRP72 4.2 82.7 1.0
CD1 B:ILE73 4.4 87.4 1.0
C B:ILE73 4.6 80.7 1.0
CG1 B:ILE73 4.6 80.2 1.0
CG1 B:VAL5 4.8 0.7 1.0
CB B:TRP72 4.9 80.4 1.0
O B:TRP72 4.9 88.7 1.0

Sodium binding site 3 out of 6 in 4hfb

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


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

b:90.0
occ:1.00
 O C:ILE71 2.5 95.0 1.0
O C:PRO68 3.0 98.6 1.0
C C:ILE71 3.7 94.2 1.0
N C:ILE73 3.7 82.2 1.0
CA C:TRP72 4.1 86.5 1.0
C C:PRO68 4.1 99.8 1.0
CB C:ILE73 4.1 80.5 1.0
CD1 C:ILE73 4.2 90.7 1.0
CG1 C:ILE73 4.2 81.4 1.0
C C:TRP72 4.2 89.1 1.0
N C:TRP72 4.3 88.1 1.0
CA C:ILE73 4.5 78.7 1.0
CG1 C:VAL5 4.6 0.3 1.0
CA C:GLU69 4.7 99.2 1.0
O C:GLU69 4.8 0.0 1.0
N C:GLU69 4.8 98.1 1.0
C C:GLU69 4.9 0.0 1.0
CA C:ILE71 4.9 93.2 1.0
N C:ILE71 4.9 94.9 1.0
O C:ILE73 4.9 84.0 1.0

Sodium binding site 4 out of 6 in 4hfb

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


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

b:0.4
occ:1.00
 O D:ILE71 2.4 0.5 1.0
O D:PRO68 3.2 0.5 1.0
C D:ILE71 3.6 0.1 1.0
N D:ILE73 3.7 91.7 1.0
CG2 D:VAL5 3.8 0.8 1.0
CA D:TRP72 3.9 97.4 1.0
N D:TRP72 4.2 99.1 1.0
C D:TRP72 4.2 99.7 1.0
CB D:ILE73 4.3 91.6 1.0
C D:PRO68 4.3 0.8 1.0
CG1 D:ILE73 4.4 93.3 1.0
CD1 D:ILE73 4.5 0.2 1.0
CA D:ILE73 4.6 89.0 1.0
O D:GLU69 4.6 0.6 1.0
CA D:GLU69 4.7 0.0 1.0
CA D:ILE71 4.8 0.3 1.0
C D:GLU69 4.9 0.5 1.0
N D:ILE71 4.9 0.3 1.0
CB D:VAL5 4.9 0.8 1.0
O D:ILE73 4.9 87.7 1.0
N D:GLU69 5.0 0.1 1.0

Sodium binding site 5 out of 6 in 4hfb

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


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

b:0.0
occ:1.00
 O E:ILE71 2.6 93.2 1.0
O E:PRO68 3.1 0.5 1.0
N E:ILE73 3.8 87.8 1.0
C E:ILE71 3.8 94.7 1.0
C E:PRO68 4.1 0.1 1.0
CB E:ILE73 4.2 86.7 1.0
CA E:TRP72 4.2 92.0 1.0
CD1 E:ILE73 4.2 96.0 1.0
CG1 E:ILE73 4.2 87.8 1.0
C E:TRP72 4.3 93.4 1.0
N E:TRP72 4.4 92.2 1.0
CA E:ILE73 4.6 84.8 1.0
CA E:GLU69 4.7 0.1 1.0
CG1 E:VAL5 4.7 0.6 1.0
N E:GLU69 4.8 0.2 1.0
O E:GLU69 4.8 0.9 1.0
C E:GLU69 4.9 0.4 1.0
O E:ILE73 4.9 85.3 1.0

Sodium binding site 6 out of 6 in 4hfb

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


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

b:0.5
occ:1.00
 OG1 E:THR226 3.8 0.8 1.0
OG1 D:THR226 4.0 0.7 1.0
OG1 A:THR226 4.4 0.9 1.0
OG1 C:THR226 4.7 0.0 1.0
CG2 E:THR226 4.8 0.3 1.0
CG2 D:THR226 4.8 0.5 1.0
OG1 B:THR226 4.9 0.3 1.0
CB E:THR226 4.9 1.0 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 15:46:53 2024

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