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Sodium in PDB 4zzb: The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon

Protein crystallography data

The structure of The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon, PDB code: 4zzb was solved by L.Sauguet, Z.Fourati, T.Prange, M.Delarue, N.Colloc'h, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 176.966, 130.528, 157.526, 90.00, 100.33, 90.00
R / Rfree (%) 21.6 / 22.3

Other elements in 4zzb:

The structure of The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon also contains other interesting chemical elements:

Xenon (Xe) 21 atoms
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon (pdb code 4zzb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon, PDB code: 4zzb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4zzb

Go back to Sodium Binding Sites List in 4zzb
Sodium binding site 1 out of 5 in the The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon


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 Locally-Closed Form Complexed to Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:0.4
occ:1.00
O A:ILE71 2.9 0.9 1.0
O A:PRO68 3.5 0.4 1.0
CG1 A:VAL5 3.5 0.8 1.0
C A:ILE71 3.7 0.2 1.0
O A:GLU69 3.8 0.9 1.0
C A:GLU69 4.2 0.8 1.0
CA A:GLU69 4.3 0.2 1.0
CA A:TRP72 4.4 0.3 1.0
N A:TRP72 4.4 0.5 1.0
C A:PRO68 4.5 0.6 1.0
N A:ILE71 4.6 0.1 1.0
CB A:VAL5 4.7 1.0 1.0
CA A:ILE71 4.7 0.4 1.0
N A:ILE73 4.8 1.0 1.0
N A:GLU69 4.9 0.0 1.0

Sodium binding site 2 out of 5 in 4zzb

Go back to Sodium Binding Sites List in 4zzb
Sodium binding site 2 out of 5 in the The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon


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 Locally-Closed Form Complexed to Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:0.6
occ:1.00
O B:ILE71 2.7 0.2 1.0
O B:PRO68 3.5 0.9 1.0
C B:ILE71 3.8 0.3 1.0
CG1 B:VAL5 4.0 0.6 1.0
CA B:TRP72 4.1 0.5 1.0
N B:ILE73 4.2 0.6 1.0
N B:TRP72 4.4 0.1 1.0
O B:GLU69 4.5 0.1 1.0
C B:PRO68 4.6 0.1 1.0
C B:TRP72 4.6 0.8 1.0
CA B:GLU69 4.7 0.2 1.0
C B:GLU69 4.8 0.0 1.0
CB B:VAL5 5.0 0.3 1.0

Sodium binding site 3 out of 5 in 4zzb

Go back to Sodium Binding Sites List in 4zzb
Sodium binding site 3 out of 5 in the The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon


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 Locally-Closed Form Complexed to Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:0.9
occ:1.00
O C:ILE71 2.8 0.5 1.0
O C:PRO68 2.9 0.9 1.0
C C:ILE71 3.9 0.4 1.0
C C:PRO68 4.0 1.0 1.0
N C:ILE73 4.2 0.0 1.0
CA C:GLU69 4.3 0.3 1.0
CA C:TRP72 4.5 0.3 1.0
O C:GLU69 4.5 0.5 1.0
N C:GLU69 4.6 0.9 1.0
C C:GLU69 4.6 0.4 1.0
N C:TRP72 4.6 0.7 1.0
CG2 C:VAL5 4.7 0.5 1.0
CB C:ILE73 4.7 0.5 1.0
CD1 C:ILE73 4.7 0.9 1.0
C C:TRP72 4.7 1.0 1.0
CG1 C:ILE73 4.8 0.7 1.0
N C:ILE71 5.0 0.8 1.0

Sodium binding site 4 out of 5 in 4zzb

Go back to Sodium Binding Sites List in 4zzb
Sodium binding site 4 out of 5 in the The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon


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 Locally-Closed Form Complexed to Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:0.3
occ:1.00
O D:ILE71 3.0 0.1 1.0
CG1 D:VAL5 3.3 0.1 1.0
O D:PRO68 3.8 0.1 1.0
C D:ILE71 4.0 0.5 1.0
O D:GLU69 4.1 0.1 1.0
CB D:VAL5 4.4 0.8 1.0
CA D:TRP72 4.4 0.8 1.0
CA D:GLU69 4.5 0.6 1.0
C D:GLU69 4.5 0.9 1.0
N D:TRP72 4.6 0.9 1.0
C D:PRO68 4.8 0.1 1.0
N D:ILE73 4.8 0.8 1.0
CA D:VAL5 4.9 0.5 1.0
N D:ILE71 5.0 0.9 1.0

Sodium binding site 5 out of 5 in 4zzb

Go back to Sodium Binding Sites List in 4zzb
Sodium binding site 5 out of 5 in the The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Glic Pentameric Ligand-Gated Ion Channel Locally-Closed Form Complexed to Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na402

b:0.2
occ:1.00
O E:ILE71 2.7 1.0 1.0
O E:PRO68 3.1 0.8 1.0
O E:GLU69 3.5 0.2 1.0
C E:ILE71 3.7 0.0 1.0
CG1 E:VAL5 3.8 1.0 1.0
C E:GLU69 3.8 0.7 1.0
CA E:GLU69 3.8 0.2 1.0
C E:PRO68 4.1 0.4 1.0
N E:GLU69 4.4 0.7 1.0
N E:ILE71 4.4 0.1 1.0
N E:TRP72 4.5 0.7 1.0
CA E:TRP72 4.6 0.6 1.0
CA E:ILE71 4.7 0.9 1.0
N E:ALA70 4.8 0.6 1.0
N E:ILE73 4.8 0.8 1.0
CB E:VAL5 5.0 0.5 1.0

Reference:

L.Sauguet, Z.Fourati, T.Prange, M.Delarue, N.Colloc'h. Structural Basis For Xenon Inhibition in A Cationic Pentameric Ligand-Gated Ion Channel. Plos One V. 11 49795 2016.
ISSN: ESSN 1932-6203
PubMed: 26910105
DOI: 10.1371/JOURNAL.PONE.0149795
Page generated: Tue Dec 15 10:10:40 2020

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