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Sodium in PDB 3igq: Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel

Protein crystallography data

The structure of Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel, PDB code: 3igq was solved by H.Nury, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.450, 130.240, 113.590, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.5

Other elements in 3igq:

The structure of Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel also contains other interesting chemical elements:

Mercury (Hg) 6 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel (pdb code 3igq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel, PDB code: 3igq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3igq

Go back to Sodium Binding Sites List in 3igq
Sodium binding site 1 out of 6 in the Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:56.3
occ:1.00
 O A:PRO68 2.2 53.9 1.0
O A:HOH226 2.3 47.0 1.0
O A:ILE71 2.4 47.1 1.0
C A:PRO68 3.4 54.5 1.0
C A:ILE71 3.7 47.3 1.0
CG1 A:ILE73 4.0 41.9 1.0
CD1 A:ILE73 4.1 41.9 1.0
CA A:GLU69 4.1 56.5 1.0
N A:ILE73 4.2 40.5 1.0
N A:GLU69 4.2 55.2 1.0
CG1 A:VAL5 4.2 68.2 1.0
CA A:PRO68 4.3 54.0 1.0
C A:GLU69 4.3 55.6 1.0
CB A:ILE73 4.4 40.3 1.0
N A:ILE71 4.4 50.6 1.0
CA A:TRP72 4.5 43.0 1.0
O A:GLU69 4.5 56.2 1.0
C A:TRP72 4.5 41.7 1.0
N A:TRP72 4.5 45.1 1.0
CA A:ILE71 4.6 48.7 1.0
CB A:PRO68 4.7 54.2 1.0
O A:HOH237 4.9 54.2 1.0
N A:ALA70 4.9 54.5 1.0
CA A:ILE73 4.9 40.2 1.0

Sodium binding site 2 out of 6 in 3igq

Go back to Sodium Binding Sites List in 3igq
Sodium binding site 2 out of 6 in the Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na801

b:56.6
occ:1.00
 O B:PRO68 2.4 54.2 1.0
O B:HOH430 2.4 51.1 1.0
O B:ILE71 2.5 47.1 1.0
C B:PRO68 3.6 54.6 1.0
C B:ILE71 3.7 47.3 1.0
N B:ILE73 4.1 40.7 1.0
CG1 B:VAL5 4.1 68.2 1.0
CG1 B:ILE73 4.2 41.6 1.0
CD1 B:ILE73 4.2 41.9 1.0
CA B:GLU69 4.3 56.4 1.0
CA B:TRP72 4.3 43.4 1.0
N B:GLU69 4.4 55.2 1.0
O B:GLU69 4.4 56.6 1.0
CB B:ILE73 4.4 40.6 1.0
C B:GLU69 4.4 55.9 1.0
N B:TRP72 4.5 45.2 1.0
C B:TRP72 4.5 42.2 1.0
N B:ILE71 4.5 50.8 1.0
CA B:PRO68 4.6 54.1 1.0
CA B:ILE71 4.7 48.4 1.0
CA B:ILE73 4.9 40.6 1.0
CB B:PRO68 5.0 54.0 1.0

Sodium binding site 3 out of 6 in 3igq

Go back to Sodium Binding Sites List in 3igq
Sodium binding site 3 out of 6 in the Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na801

b:56.7
occ:1.00
 O C:ILE71 2.2 47.3 1.0
O C:PRO68 2.4 54.2 1.0
O C:HOH234 2.6 53.0 1.0
C C:ILE71 3.5 47.4 1.0
C C:PRO68 3.6 54.8 1.0
CG1 C:ILE73 4.0 41.9 1.0
N C:ILE73 4.1 40.7 1.0
CG1 C:VAL5 4.1 68.0 1.0
CD1 C:ILE73 4.2 41.9 1.0
CA C:TRP72 4.2 43.5 1.0
CA C:GLU69 4.3 56.6 1.0
N C:TRP72 4.3 44.9 1.0
CB C:ILE73 4.3 40.1 1.0
N C:GLU69 4.4 55.5 1.0
C C:TRP72 4.4 42.0 1.0
N C:ILE71 4.4 50.7 1.0
C C:GLU69 4.4 55.8 1.0
O C:GLU69 4.4 56.7 1.0
CA C:ILE71 4.5 48.5 1.0
CA C:PRO68 4.5 54.3 1.0
CA C:ILE73 4.8 40.1 1.0
N C:ALA70 5.0 54.9 1.0
CB C:PRO68 5.0 54.2 1.0

Sodium binding site 4 out of 6 in 3igq

Go back to Sodium Binding Sites List in 3igq
Sodium binding site 4 out of 6 in the Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na801

b:55.6
occ:1.00
 O D:ILE71 2.4 47.2 1.0
O D:HOH205 2.4 41.2 1.0
O D:PRO68 2.5 54.3 1.0
C D:ILE71 3.6 47.1 1.0
C D:PRO68 3.6 54.7 1.0
CG1 D:VAL5 4.0 68.0 1.0
CG1 D:ILE73 4.2 41.9 1.0
N D:ILE73 4.2 40.6 1.0
CD1 D:ILE73 4.2 41.8 1.0
CA D:GLU69 4.2 56.7 1.0
CA D:TRP72 4.3 43.1 1.0
C D:GLU69 4.4 55.9 1.0
O D:GLU69 4.4 56.5 1.0
N D:GLU69 4.4 55.5 1.0
N D:TRP72 4.4 45.0 1.0
N D:ILE71 4.4 51.0 1.0
CB D:ILE73 4.4 40.3 1.0
C D:TRP72 4.6 41.9 1.0
CA D:PRO68 4.6 54.2 1.0
CA D:ILE71 4.6 48.5 1.0
O D:HOH225 4.9 46.9 1.0
CA D:ILE73 4.9 40.0 1.0
N D:ALA70 5.0 54.8 1.0
CB D:PRO68 5.0 54.2 1.0

Sodium binding site 5 out of 6 in 3igq

Go back to Sodium Binding Sites List in 3igq
Sodium binding site 5 out of 6 in the Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na801

b:55.7
occ:1.00
 O E:PRO68 2.1 54.3 1.0
O E:HOH403 2.3 50.4 1.0
O E:ILE71 2.3 46.5 1.0
C E:PRO68 3.3 54.5 1.0
C E:ILE71 3.5 46.8 1.0
CD1 E:ILE73 4.0 42.0 1.0
CG1 E:ILE73 4.0 42.0 1.0
CA E:GLU69 4.0 56.6 1.0
N E:GLU69 4.1 55.3 1.0
C E:GLU69 4.2 55.6 1.0
N E:ILE71 4.2 50.9 1.0
N E:ILE73 4.2 40.8 1.0
CG1 E:VAL5 4.3 68.3 1.0
CA E:PRO68 4.3 54.2 1.0
N E:TRP72 4.3 44.8 1.0
CA E:TRP72 4.3 43.3 1.0
O E:GLU69 4.3 56.1 1.0
CA E:ILE71 4.4 48.4 1.0
CB E:ILE73 4.5 40.3 1.0
C E:TRP72 4.5 42.1 1.0
N E:ALA70 4.7 54.4 1.0
CB E:PRO68 4.8 54.1 1.0
CA E:ILE73 5.0 40.4 1.0

Sodium binding site 6 out of 6 in 3igq

Go back to Sodium Binding Sites List in 3igq
Sodium binding site 6 out of 6 in the Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na801

b:55.9
occ:1.00
 O F:ILE71 2.3 47.3 1.0
O F:PRO68 2.3 54.1 1.0
O F:HOH245 2.5 45.3 1.0
O F:HOH237 2.6 51.6 1.0
C F:PRO68 3.5 54.6 1.0
C F:ILE71 3.6 47.1 1.0
CG1 F:ILE73 4.0 42.1 1.0
N F:ILE73 4.1 40.1 1.0
CD1 F:ILE73 4.1 41.7 1.0
CG1 F:VAL5 4.1 68.0 1.0
CA F:GLU69 4.2 56.3 1.0
CB F:ILE73 4.3 40.1 1.0
CA F:TRP72 4.3 43.4 1.0
N F:GLU69 4.3 55.4 1.0
N F:TRP72 4.4 44.7 1.0
C F:GLU69 4.4 55.6 1.0
C F:TRP72 4.4 41.9 1.0
N F:ILE71 4.5 50.5 1.0
O F:GLU69 4.5 56.1 1.0
CA F:PRO68 4.5 54.1 1.0
CA F:ILE71 4.6 48.5 1.0
O F:HOH208 4.8 56.3 1.0
CA F:ILE73 4.8 40.0 1.0
CB F:PRO68 4.9 53.9 1.0
N F:ALA70 5.0 54.6 1.0

Reference:

H.Nury, N.Bocquet, C.Le Poupon, B.Raynal, A.Haouz, P.-J.Corringer, M.Delarue. Crystal Structure of the Extracellular Domain of A Bacterial Ligand-Gated Ion Channel J.Mol.Biol. V. 395 1114 2010.
ISSN: ISSN 0022-2836
PubMed: 19917292
DOI: 10.1016/J.JMB.2009.11.024
Page generated: Mon Oct 7 10:56:58 2024

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