Atomistry » Sodium » PDB 3icf-3ivu » 3igq
Atomistry »
  Sodium »
    PDB 3icf-3ivu »
      3igq »

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

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