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Sodium in PDB 6f10: Glic Mutant D88N

Protein crystallography data

The structure of Glic Mutant D88N, PDB code: 6f10 was solved by H.D.Hu, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.370, 134.810, 160.680, 90.00, 103.12, 90.00
R / Rfree (%) 20.7 / 22.3

Other elements in 6f10:

The structure of Glic Mutant D88N also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Glic Mutant D88N (pdb code 6f10). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Glic Mutant D88N, PDB code: 6f10:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6f10

Go back to Sodium Binding Sites List in 6f10
Sodium binding site 1 out of 6 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:0.7
occ:1.00
 O A:ILE71 2.6 0.3 1.0
O A:PRO68 3.1 0.5 1.0
N A:ILE73 3.6 0.3 1.0
C A:ILE71 3.7 0.5 1.0
CA A:TRP72 4.0 0.2 1.0
CD1 A:ILE73 4.1 0.7 1.0
C A:TRP72 4.2 0.6 1.0
CB A:ILE73 4.2 0.6 1.0
C A:PRO68 4.2 0.1 1.0
N A:TRP72 4.3 0.1 1.0
CG1 A:ILE73 4.4 0.1 1.0
CA A:ILE73 4.5 0.9 1.0
O A:GLU69 4.6 0.4 1.0
O A:ILE73 4.8 0.8 1.0
N A:GLU69 4.9 0.9 1.0
C A:GLU69 4.9 0.9 1.0
CA A:ILE71 4.9 0.5 1.0
CA A:GLU69 5.0 0.3 1.0

Sodium binding site 2 out of 6 in 6f10

Go back to Sodium Binding Sites List in 6f10
Sodium binding site 2 out of 6 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:0.5
occ:1.00
 O B:ILE71 2.5 0.6 1.0
O B:PRO68 3.1 0.2 1.0
N B:ILE73 3.6 0.7 1.0
C B:ILE71 3.7 0.6 1.0
CA B:TRP72 4.0 0.6 1.0
CD1 B:ILE73 4.1 0.2 1.0
CB B:ILE73 4.1 0.1 1.0
C B:TRP72 4.2 0.6 1.0
C B:PRO68 4.2 0.7 1.0
CG1 B:ILE73 4.2 0.6 1.0
N B:TRP72 4.3 0.3 1.0
CA B:ILE73 4.4 0.6 1.0
O B:ILE73 4.7 0.8 1.0
O B:GLU69 4.8 0.7 1.0
N B:GLU69 4.9 0.2 1.0
CA B:ILE71 4.9 0.5 1.0
CA B:GLU69 4.9 0.8 1.0

Sodium binding site 3 out of 6 in 6f10

Go back to Sodium Binding Sites List in 6f10
Sodium binding site 3 out of 6 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:0.0
occ:1.00
 OG1 C:THR226 3.7 0.8 1.0
OG1 D:THR226 3.8 0.6 1.0
OG1 B:THR226 4.0 1.0 1.0
OG1 E:THR226 4.1 0.0 1.0
OG1 A:THR226 4.2 0.3 1.0
CG2 C:THR226 4.7 0.9 1.0
CB C:THR226 4.8 0.5 1.0

Sodium binding site 4 out of 6 in 6f10

Go back to Sodium Binding Sites List in 6f10
Sodium binding site 4 out of 6 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:0.7
occ:1.00
 O C:ILE71 2.7 0.4 1.0
O C:PRO68 3.0 0.6 1.0
N C:ILE73 3.7 0.7 1.0
C C:ILE71 3.8 0.7 1.0
CD1 C:ILE73 4.0 0.3 1.0
CA C:TRP72 4.1 0.8 1.0
C C:PRO68 4.1 0.0 1.0
CB C:ILE73 4.1 0.1 1.0
C C:TRP72 4.3 1.0 1.0
CG1 C:ILE73 4.3 0.6 1.0
N C:TRP72 4.4 0.8 1.0
CA C:ILE73 4.5 1.0 1.0
O C:GLU69 4.8 0.3 1.0
O C:ILE73 4.8 0.2 1.0
N C:GLU69 4.9 0.2 1.0
CA C:GLU69 4.9 0.9 1.0

Sodium binding site 5 out of 6 in 6f10

Go back to Sodium Binding Sites List in 6f10
Sodium binding site 5 out of 6 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:0.6
occ:1.00
 O D:ILE71 2.5 0.3 1.0
O D:PRO68 3.0 0.8 1.0
N D:ILE73 3.7 0.2 1.0
C D:ILE71 3.7 0.8 1.0
CA D:TRP72 4.0 0.2 1.0
CD1 D:ILE73 4.1 0.8 1.0
C D:PRO68 4.1 0.4 1.0
CB D:ILE73 4.1 0.1 1.0
C D:TRP72 4.2 0.9 1.0
N D:TRP72 4.3 0.1 1.0
CG1 D:ILE73 4.4 0.3 1.0
CA D:ILE73 4.5 0.6 1.0
O D:GLU69 4.8 0.7 1.0
O D:ILE73 4.8 0.0 1.0
N D:GLU69 4.9 0.0 1.0
CA D:GLU69 4.9 0.2 1.0
CA D:ILE71 4.9 0.9 1.0
C D:GLU69 5.0 0.2 1.0

Sodium binding site 6 out of 6 in 6f10

Go back to Sodium Binding Sites List in 6f10
Sodium binding site 6 out of 6 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na403

b:0.1
occ:1.00
 O E:ILE71 2.8 0.7 1.0
O E:PRO68 3.1 0.9 1.0
N E:ILE73 3.6 0.4 1.0
C E:ILE71 3.9 0.9 1.0
CB E:ILE73 4.0 0.5 1.0
CD1 E:ILE73 4.1 0.7 1.0
CA E:TRP72 4.1 0.7 1.0
C E:PRO68 4.2 0.9 1.0
C E:TRP72 4.2 0.1 1.0
CG1 E:ILE73 4.3 0.9 1.0
CA E:ILE73 4.4 0.8 1.0
N E:TRP72 4.5 0.5 1.0
O E:ILE73 4.7 0.4 1.0
N E:GLU69 5.0 0.6 1.0
O E:GLU69 5.0 0.9 1.0

Reference:

A.Nemecz, H.Hu, Z.Fourati, C.Van Renterghem, M.Delarue, P.J.Corringer. Full Mutational Mapping of Titratable Residues Helps to Identify Proton-Sensors Involved in the Control of Channel Gating in the Gloeobacter Violaceus Pentameric Ligand-Gated Ion Channel. Plos Biol. V. 15 04470 2017.
ISSN: ESSN 1545-7885
PubMed: 29281623
DOI: 10.1371/JOURNAL.PBIO.2004470
Page generated: Tue Oct 8 08:36:03 2024

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