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Sodium in PDB 4hfi: The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution

Protein crystallography data

The structure of The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution, PDB code: 4hfi was solved by L.Sauguet, P.J.Corringer, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.05 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.890, 133.200, 160.200, 90.00, 102.74, 90.00
R / Rfree (%) 20.5 / 21.6

Other elements in 4hfi:

The structure of The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution 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 at 2.4 A Resolution (pdb code 4hfi). 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 at 2.4 A Resolution, PDB code: 4hfi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4hfi

Go back to Sodium Binding Sites List in 4hfi
Sodium binding site 1 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:78.1
occ:1.00
O A:ILE71 2.5 83.1 1.0
O A:PRO68 3.2 0.0 1.0
N A:ILE73 3.5 72.7 1.0
C A:ILE71 3.7 83.8 1.0
CA A:TRP72 3.8 76.5 1.0
C A:TRP72 4.0 78.2 1.0
CG2 A:VAL5 4.0 0.8 1.0
CB A:ILE73 4.1 73.8 1.0
N A:TRP72 4.2 78.2 1.0
C A:PRO68 4.3 0.8 1.0
CA A:ILE73 4.4 71.0 1.0
CG1 A:ILE73 4.4 74.6 1.0
CD1 A:ILE73 4.4 81.4 1.0
O A:ILE73 4.7 71.4 1.0
CA A:GLU69 4.8 95.5 1.0
O A:GLU69 4.8 96.7 1.0
CA A:ILE71 4.9 83.5 1.0
C A:GLU69 4.9 97.1 1.0
N A:GLU69 5.0 96.2 1.0

Sodium binding site 2 out of 6 in 4hfi

Go back to Sodium Binding Sites List in 4hfi
Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:88.8
occ:1.00
O D:HOH535 3.3 85.9 1.0
O C:HOH511 3.4 83.0 1.0
O E:HOH520 3.6 72.3 1.0
O A:HOH518 3.7 76.0 1.0
O B:HOH524 3.8 76.0 1.0
OG1 C:THR226 4.1 59.4 1.0
OG1 D:THR226 4.2 54.4 1.0
OG1 B:THR226 4.4 56.2 1.0
OG1 E:THR226 4.4 61.1 1.0
OG1 A:THR226 4.5 61.0 1.0

Sodium binding site 3 out of 6 in 4hfi

Go back to Sodium Binding Sites List in 4hfi
Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:79.9
occ:1.00
O B:ILE71 2.5 70.4 1.0
N B:ILE73 3.2 62.9 1.0
O B:PRO68 3.4 83.4 1.0
C B:ILE71 3.6 70.3 1.0
CA B:TRP72 3.6 64.3 1.0
C B:TRP72 3.8 67.1 1.0
CG2 B:VAL5 4.0 0.3 1.0
N B:TRP72 4.0 65.3 1.0
CB B:ILE73 4.1 64.3 1.0
CA B:ILE73 4.2 61.5 1.0
CD1 B:ILE73 4.2 71.1 1.0
O B:ILE73 4.5 64.8 1.0
C B:PRO68 4.5 84.5 1.0
CG1 B:ILE73 4.6 64.8 1.0
O B:TRP72 4.9 66.7 1.0
CA B:ILE71 4.9 68.5 1.0
C B:ILE73 4.9 64.7 1.0
O B:GLU69 4.9 83.2 1.0
CB B:TRP72 4.9 63.0 1.0
CB B:VAL5 5.0 0.7 1.0
CA B:GLU69 5.0 81.4 1.0

Sodium binding site 4 out of 6 in 4hfi

Go back to Sodium Binding Sites List in 4hfi
Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na406

b:73.0
occ:1.00
O C:ILE71 2.9 80.0 1.0
N C:ILE73 3.3 69.1 1.0
O C:PRO68 3.7 95.3 1.0
CA C:TRP72 3.8 72.4 1.0
C C:TRP72 3.9 74.1 1.0
C C:ILE71 3.9 80.0 1.0
CB C:ILE73 4.0 69.8 1.0
CG2 C:VAL5 4.0 0.6 1.0
CA C:ILE73 4.1 67.2 1.0
N C:TRP72 4.3 73.9 1.0
O C:ILE73 4.3 69.8 1.0
CG1 C:ILE73 4.4 70.0 1.0
CD1 C:ILE73 4.5 77.2 1.0
C C:ILE73 4.8 69.9 1.0
C C:PRO68 4.8 96.4 1.0

Sodium binding site 5 out of 6 in 4hfi

Go back to Sodium Binding Sites List in 4hfi
Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na406

b:86.3
occ:1.00
O D:ILE71 3.1 84.4 1.0
N D:ILE73 3.5 71.5 1.0
CG2 D:VAL5 3.7 0.3 1.0
CA D:TRP72 3.9 76.4 1.0
O D:PRO68 4.1 0.1 1.0
C D:TRP72 4.1 77.2 1.0
C D:ILE71 4.1 85.0 1.0
O D:ILE73 4.4 70.1 1.0
CB D:ILE73 4.4 72.4 1.0
CA D:ILE73 4.4 69.5 1.0
N D:TRP72 4.4 78.5 1.0
CB D:VAL5 4.8 0.7 1.0
CG1 D:ILE73 4.9 73.0 1.0
C D:ILE73 4.9 70.4 1.0
CB D:TRP72 5.0 74.9 1.0
CD1 D:TRP72 5.0 78.2 1.0

Sodium binding site 6 out of 6 in 4hfi

Go back to Sodium Binding Sites List in 4hfi
Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na406

b:76.5
occ:1.00
O E:ILE71 2.5 78.1 1.0
O E:PRO68 3.1 90.8 1.0
N E:ILE73 3.6 69.8 1.0
C E:ILE71 3.6 78.5 1.0
CA E:TRP72 3.9 71.3 1.0
CG2 E:VAL5 4.0 0.4 1.0
C E:TRP72 4.1 73.6 1.0
CB E:ILE73 4.2 71.0 1.0
N E:TRP72 4.2 72.7 1.0
C E:PRO68 4.2 91.9 1.0
CD1 E:ILE73 4.3 80.2 1.0
CG1 E:ILE73 4.3 71.3 1.0
CA E:ILE73 4.5 68.3 1.0
CA E:GLU69 4.7 88.1 1.0
O E:GLU69 4.7 90.2 1.0
N E:GLU69 4.9 88.2 1.0
C E:GLU69 4.9 90.1 1.0
CA E:ILE71 4.9 77.9 1.0
O E:ILE73 4.9 72.2 1.0
N E:ILE71 5.0 79.7 1.0

Reference:

L.Sauguet, F.Poitevin, S.Murail, C.Van Renterghem, G.Moraga-Cid, L.Malherbe, A.W.Thompson, P.Koehl, P.J.Corringer, M.Baaden, M.Delarue. Structural Basis For Ion Permeation Mechanism in Pentameric Ligand-Gated Ion Channels. Embo J. V. 32 728 2013.
ISSN: ISSN 0261-4189
PubMed: 23403925
DOI: 10.1038/EMBOJ.2013.17
Page generated: Tue Dec 15 06:43:19 2020

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