Atomistry » Sodium » PDB 4iic-4j0n » 4ilb
Atomistry »
  Sodium »
    PDB 4iic-4j0n »
      4ilb »

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

Go back to Sodium Binding Sites List in 4ilb
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

Go back to Sodium Binding Sites List in 4ilb
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

Go back to Sodium Binding Sites List in 4ilb
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

Go back to Sodium Binding Sites List in 4ilb
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy