Atomistry » Sodium » PDB 4q3d-4qom » 4qh5
Atomistry »
  Sodium »
    PDB 4q3d-4qom »
      4qh5 »

Sodium in PDB 4qh5: The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Crystallized in Phosphate Buffer

Protein crystallography data

The structure of The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Crystallized in Phosphate Buffer, PDB code: 4qh5 was solved by Z.Fourati, M.Delarue, L.Sauguet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.878, 134.423, 160.003, 90.00, 102.72, 90.00
R / Rfree (%) 19.9 / 21.6

Other elements in 4qh5:

The structure of The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Crystallized in Phosphate Buffer also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Crystallized in Phosphate Buffer (pdb code 4qh5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Crystallized in Phosphate Buffer, PDB code: 4qh5:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4qh5

Go back to Sodium Binding Sites List in 4qh5
Sodium binding site 1 out of 4 in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Crystallized in Phosphate Buffer


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 (Wild-Type) Crystallized in Phosphate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:0.4
occ:1.00
O B:ILE71 2.4 0.8 1.0
O B:PRO68 3.2 0.0 1.0
C B:ILE71 3.6 0.8 1.0
N B:ILE73 3.7 0.0 1.0
CG1 B:ILE73 3.9 0.8 1.0
CD1 B:ILE73 4.0 0.2 1.0
CA B:TRP72 4.0 0.6 1.0
CA B:GLU69 4.1 0.2 1.0
C B:PRO68 4.1 0.9 1.0
N B:TRP72 4.2 0.3 1.0
CB B:ILE73 4.2 0.1 1.0
C B:TRP72 4.3 0.8 1.0
O B:GLU69 4.3 0.4 1.0
C B:GLU69 4.4 0.8 1.0
N B:GLU69 4.5 0.3 1.0
CA B:ILE73 4.6 0.2 1.0
N B:ILE71 4.7 0.4 1.0
CG2 B:VAL5 4.7 0.8 1.0
CA B:ILE71 4.7 0.3 1.0

Sodium binding site 2 out of 4 in 4qh5

Go back to Sodium Binding Sites List in 4qh5
Sodium binding site 2 out of 4 in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Crystallized in Phosphate Buffer


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 (Wild-Type) Crystallized in Phosphate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:91.9
occ:1.00
OG1 D:THR226 3.8 77.7 1.0
OG1 C:THR226 3.8 86.1 1.0
OG1 E:THR226 3.9 79.3 1.0
OG1 B:THR226 4.0 81.5 1.0
OG1 A:THR226 4.1 89.7 1.0
CG2 D:THR226 4.8 78.9 1.0
CB D:THR226 4.9 81.2 1.0
CG2 C:THR226 4.9 75.1 1.0
CB C:THR226 5.0 80.0 1.0
CG2 E:THR226 5.0 72.3 1.0

Sodium binding site 3 out of 4 in 4qh5

Go back to Sodium Binding Sites List in 4qh5
Sodium binding site 3 out of 4 in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Crystallized in Phosphate Buffer


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 (Wild-Type) Crystallized in Phosphate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:89.8
occ:1.00
O C:ILE71 2.8 0.7 1.0
O C:PRO68 3.2 0.0 1.0
CD1 C:ILE73 3.8 0.1 1.0
CG1 C:ILE73 3.9 0.9 1.0
N C:ILE73 3.9 0.2 1.0
C C:ILE71 3.9 0.4 1.0
C C:PRO68 4.0 1.0 1.0
CA C:GLU69 4.0 0.5 1.0
CB C:ILE73 4.2 0.0 1.0
N C:GLU69 4.3 0.2 1.0
O C:GLU69 4.4 0.6 1.0
CA C:TRP72 4.4 0.9 1.0
C C:GLU69 4.4 0.5 1.0
C C:TRP72 4.5 0.4 1.0
N C:TRP72 4.6 0.6 1.0
CA C:ILE73 4.7 0.9 1.0
CG2 C:VAL5 4.9 0.8 1.0
N C:ILE71 5.0 0.6 1.0

Sodium binding site 4 out of 4 in 4qh5

Go back to Sodium Binding Sites List in 4qh5
Sodium binding site 4 out of 4 in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Crystallized in Phosphate Buffer


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 (Wild-Type) Crystallized in Phosphate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:0.4
occ:1.00
O D:ILE71 2.2 0.6 1.0
C D:ILE71 3.3 0.5 1.0
N D:ILE73 3.4 0.8 1.0
O D:PRO68 3.5 1.0 1.0
CA D:TRP72 3.6 0.2 1.0
CG1 D:ILE73 3.8 0.3 1.0
C D:TRP72 3.9 0.7 1.0
N D:TRP72 3.9 0.1 1.0
CD1 D:ILE73 4.0 0.4 1.0
CB D:ILE73 4.1 0.2 1.0
CA D:ILE73 4.3 0.7 1.0
C D:PRO68 4.5 0.4 1.0
CA D:GLU69 4.5 0.5 1.0
O D:GLU69 4.5 0.1 1.0
CG2 D:VAL5 4.6 0.7 1.0
CA D:ILE71 4.6 0.3 1.0
C D:GLU69 4.7 0.3 1.0
N D:ILE71 4.7 0.1 1.0
O D:ILE73 4.9 0.8 1.0
N D:GLU69 4.9 0.2 1.0
CB D:VAL5 4.9 0.4 1.0
O D:TRP72 4.9 0.6 1.0
CB D:TRP72 4.9 0.7 1.0

Reference:

Z.Fourati, L.Sauguet, M.Delarue. Structural Characterization of Potential Modulation Sites in the Extracellular Domain of the Prokaryotic Pentameric Proton-Gated Ion Channel Glic Acta Crystallogr.,Sect.D 2015.
ISSN: ESSN 1399-0047
Page generated: Mon Oct 7 17:59:56 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