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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: Tue Dec 15 07:05:34 2020

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