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Sodium in PDB 4ilb: The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium

Protein crystallography data

The structure of The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium, PDB code: 4ilb 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) 36.37 / 3.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 180.984, 132.412, 159.884, 90.00, 102.09, 90.00
R / Rfree (%) 20.5 / 22.6

Other elements in 4ilb:

The structure of The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium also contains other interesting chemical elements:

Rubidium (Rb) 1 atom
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium (pdb code 4ilb). 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 Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium, PDB code: 4ilb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4ilb

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Sodium binding site 1 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:56.3
occ:1.00
 O A:ILE71 2.4 67.5 1.0
O A:PRO68 3.1 78.3 1.0
C A:ILE71 3.6 67.4 1.0
N A:ILE73 3.7 60.0 1.0
CA A:TRP72 3.9 61.8 1.0
CG2 A:VAL5 3.9 81.3 1.0
C A:TRP72 4.2 65.4 1.0
N A:TRP72 4.2 63.0 1.0
C A:PRO68 4.2 79.2 1.0
CB A:ILE73 4.3 60.3 1.0
CG1 A:ILE73 4.4 60.3 1.0
CD1 A:ILE73 4.4 66.6 1.0
O A:GLU69 4.4 74.5 1.0
CA A:ILE73 4.6 57.9 1.0
CA A:GLU69 4.6 74.7 1.0
C A:GLU69 4.7 75.3 1.0
CA A:ILE71 4.8 64.2 1.0
N A:GLU69 4.8 75.4 1.0
N A:ILE71 4.8 65.5 1.0
O A:ILE73 5.0 58.5 1.0

Sodium binding site 2 out of 6 in 4ilb

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Sodium binding site 2 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na408

b:58.9
occ:1.00
 O B:ILE71 2.5 63.5 1.0
O B:PRO68 2.9 63.9 1.0
N B:ILE73 3.7 54.1 1.0
C B:ILE71 3.7 61.7 1.0
C B:PRO68 4.0 65.8 1.0
CA B:TRP72 4.0 54.9 1.0
CD1 B:ILE73 4.1 52.2 1.0
C B:TRP72 4.2 59.1 1.0
CB B:ILE73 4.2 54.5 1.0
N B:TRP72 4.3 56.0 1.0
CA B:ILE73 4.5 52.2 1.0
CA B:GLU69 4.5 63.5 1.0
O B:GLU69 4.5 65.4 1.0
CG1 B:ILE73 4.6 53.8 1.0
N B:GLU69 4.7 63.5 1.0
C B:GLU69 4.7 66.0 1.0
CG2 B:VAL5 4.8 94.7 1.0
CA B:ILE71 4.8 58.1 1.0
N B:ILE71 4.9 59.9 1.0
O B:ILE73 4.9 53.1 1.0

Sodium binding site 3 out of 6 in 4ilb

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Sodium binding site 3 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na407

b:49.7
occ:1.00
 O C:ILE71 2.3 69.2 1.0
O C:PRO68 2.7 69.8 1.0
C C:ILE71 3.5 68.2 1.0
O C:GLU69 3.7 67.7 1.0
C C:PRO68 3.8 70.7 1.0
CA C:GLU69 3.9 67.8 1.0
CG2 C:VAL5 3.9 96.1 1.0
C C:GLU69 4.0 69.5 1.0
N C:GLU69 4.2 67.9 1.0
CA C:TRP72 4.3 62.3 1.0
N C:ILE73 4.3 60.0 1.0
N C:TRP72 4.3 63.3 1.0
N C:ILE71 4.4 64.5 1.0
CA C:ILE71 4.5 64.2 1.0
CD1 C:ILE73 4.6 70.3 1.0
C C:TRP72 4.7 65.4 1.0
CG1 C:ILE73 4.7 60.8 1.0
CB C:ILE73 4.8 60.6 1.0
N C:ALA70 4.9 65.5 1.0
CB C:VAL5 5.0 96.2 1.0

Sodium binding site 4 out of 6 in 4ilb

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Sodium binding site 4 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na407

b:56.0
occ:1.00
 OE2 D:GLU222 3.2 86.1 0.5
OE2 B:GLU222 4.0 71.2 0.5
OE2 E:GLU222 4.2 84.2 0.5
OG1 D:THR226 4.3 46.1 1.0
OG1 C:THR226 4.3 50.6 1.0
OE2 A:GLU222 4.3 83.7 0.5
CD D:GLU222 4.4 84.8 0.5
OE2 C:GLU222 4.4 66.5 0.5
OG1 E:THR226 4.5 48.0 1.0
OG1 A:THR226 4.7 47.2 1.0
OG1 B:THR226 4.8 48.6 1.0

Sodium binding site 5 out of 6 in 4ilb

Go back to Sodium Binding Sites List in 4ilb
Sodium binding site 5 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na408

b:62.7
occ:1.00
 O D:ILE71 2.5 68.9 1.0
N D:ILE73 3.3 57.6 1.0
O D:PRO68 3.4 75.3 1.0
C D:ILE71 3.6 67.1 1.0
CA D:TRP72 3.7 57.5 1.0
CG2 D:VAL5 3.9 83.4 1.0
C D:TRP72 3.9 62.8 1.0
CB D:ILE73 4.0 57.5 1.0
N D:TRP72 4.1 59.6 1.0
CA D:ILE73 4.3 55.3 1.0
CG1 D:ILE73 4.3 57.8 1.0
CD1 D:ILE73 4.4 66.2 1.0
C D:PRO68 4.5 76.8 1.0
O D:ILE73 4.6 58.3 1.0
O D:GLU69 4.8 74.4 1.0
CA D:ILE71 4.9 64.2 1.0
CB D:VAL5 4.9 83.4 1.0
O D:TRP72 4.9 63.3 1.0
CA D:GLU69 5.0 72.2 1.0
CB D:TRP72 5.0 54.8 1.0
C D:ILE73 5.0 57.6 1.0

Sodium binding site 6 out of 6 in 4ilb

Go back to Sodium Binding Sites List in 4ilb
Sodium binding site 6 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Rubidium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na407

b:70.2
occ:1.00
 O E:ILE71 2.5 65.8 1.0
O E:PRO68 2.8 74.6 1.0
C E:ILE71 3.7 64.9 1.0
N E:ILE73 3.8 54.6 1.0
C E:PRO68 3.8 75.8 1.0
CD1 E:ILE73 4.0 59.0 1.0
CG1 E:ILE73 4.1 56.2 1.0
CB E:ILE73 4.1 56.3 1.0
CA E:TRP72 4.2 56.1 1.0
C E:TRP72 4.3 60.1 1.0
CG2 E:VAL5 4.4 91.6 1.0
N E:TRP72 4.4 58.2 1.0
CA E:GLU69 4.5 72.4 1.0
N E:GLU69 4.5 72.7 1.0
CA E:ILE73 4.6 53.5 1.0
O E:GLU69 4.6 75.4 1.0
C E:GLU69 4.7 74.9 1.0
CA E:ILE71 4.8 63.6 1.0
N E:ILE71 4.8 65.5 1.0
CA E:PRO68 4.9 71.6 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: Mon Oct 7 16:02:49 2024

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