Sodium in PDB 6f0u: Glic Mutant E35A

The structure of Glic Mutant E35A, PDB code: 6f0u 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)	27.14 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.840, 133.060, 158.390, 90.00, 101.53, 90.00
R / Rfree (%)	21.8 / 23.3

The structure of Glic Mutant E35A also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Glic Mutant E35A (pdb code 6f0u). 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 E35A, PDB code: 6f0u:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Glic Mutant E35A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glic Mutant E35A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:89.1 occ:1.00 O A:ILE71 2.2 71.4 1.0 O A:HOH516 2.6 49.3 1.0 O A:PRO68 2.8 88.0 1.0 C A:ILE71 3.4 73.2 1.0 N A:ILE73 3.7 64.1 1.0 C A:PRO68 3.9 89.4 1.0 CA A:TRP72 4.1 66.5 1.0 CG2 A:VAL5 4.1 95.6 1.0 CD1 A:ILE73 4.1 69.8 1.0 N A:TRP72 4.2 68.2 1.0 CB A:ILE73 4.2 64.4 1.0 C A:TRP72 4.3 69.6 1.0 CG1 A:ILE73 4.3 65.5 1.0 O A:GLU69 4.3 89.7 1.0 CA A:GLU69 4.5 87.0 1.0 N A:ILE71 4.5 77.4 1.0 C A:GLU69 4.5 89.8 1.0 CA A:ILE71 4.6 74.5 1.0 N A:GLU69 4.6 86.9 1.0 CA A:ILE73 4.6 62.3 1.0 CA A:PRO68 5.0 85.0 1.0

Sodium binding site 2 out of 6 in the Glic Mutant E35A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Glic Mutant E35A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:87.6 occ:1.00 O B:ILE71 2.6 68.5 1.0 O B:PRO68 3.2 84.6 1.0 C B:ILE71 3.7 68.2 1.0 N B:ILE73 3.8 62.2 1.0 CG2 B:VAL5 4.1 0.7 1.0 CA B:TRP72 4.1 61.9 1.0 C B:PRO68 4.3 84.8 1.0 C B:TRP72 4.3 67.6 1.0 N B:TRP72 4.4 62.6 1.0 CB B:ILE73 4.4 60.8 1.0 O B:GLU69 4.4 85.3 1.0 CD1 B:ILE73 4.5 70.1 1.0 CG1 B:ILE73 4.6 61.5 1.0 CA B:ILE73 4.6 59.1 1.0 CA B:GLU69 4.7 82.3 1.0 C B:GLU69 4.7 83.4 1.0 N B:GLU69 4.9 82.5 1.0 N B:ILE71 4.9 69.3 1.0 CA B:ILE71 4.9 67.2 1.0 O B:ILE73 4.9 63.3 1.0

Sodium binding site 3 out of 6 in the Glic Mutant E35A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Glic Mutant E35A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:91.3 occ:1.00 O B:HOH522 2.2 86.1 1.0 OG1 D:THR226 3.6 65.2 1.0 OG1 C:THR226 3.9 62.5 1.0 CG2 C:THR226 4.3 55.2 1.0 OG1 E:THR226 4.3 65.4 1.0 CG2 D:THR226 4.5 52.5 1.0 CB D:THR226 4.7 61.2 1.0 CB C:THR226 4.7 60.6 1.0 OG1 B:THR226 4.9 58.6 1.0 OG1 A:THR226 4.9 61.3 1.0

Sodium binding site 4 out of 6 in the Glic Mutant E35A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Glic Mutant E35A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na404 b:79.8 occ:1.00 O C:ILE71 2.4 72.3 1.0 O C:PRO68 3.1 82.1 1.0 N C:ILE73 3.6 62.3 1.0 C C:ILE71 3.6 72.4 1.0 CA C:TRP72 4.0 65.3 1.0 CB C:ILE73 4.1 60.6 1.0 CG2 C:VAL5 4.1 94.1 1.0 C C:TRP72 4.2 67.0 1.0 C C:PRO68 4.2 83.4 1.0 CD1 C:ILE73 4.2 66.5 1.0 N C:TRP72 4.2 66.0 1.0 CG1 C:ILE73 4.2 61.1 1.0 CA C:ILE73 4.4 59.0 1.0 O C:GLU69 4.7 85.2 1.0 CA C:GLU69 4.8 81.8 1.0 CA C:ILE71 4.8 73.3 1.0 N C:ILE71 4.8 75.5 1.0 O C:ILE73 4.8 63.8 1.0 C C:GLU69 4.8 85.1 1.0 N C:GLU69 4.9 81.5 1.0

Sodium binding site 5 out of 6 in the Glic Mutant E35A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Glic Mutant E35A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:99.9 occ:1.00 O D:ILE71 2.5 76.3 1.0 O D:PRO68 2.9 87.4 1.0 C D:ILE71 3.7 76.2 1.0 C D:PRO68 3.9 88.0 1.0 CG2 D:VAL5 4.0 0.4 1.0 N D:ILE73 4.1 67.8 1.0 O D:GLU69 4.2 87.1 1.0 CA D:GLU69 4.3 83.8 1.0 CA D:TRP72 4.3 68.4 1.0 C D:GLU69 4.4 86.3 1.0 CD1 D:ILE73 4.4 76.3 1.0 N D:TRP72 4.5 70.2 1.0 N D:GLU69 4.5 84.2 1.0 CB D:ILE73 4.5 68.8 1.0 C D:TRP72 4.6 74.0 1.0 CG1 D:ILE73 4.6 69.8 1.0 N D:ILE71 4.6 77.2 1.0 CA D:ILE71 4.8 75.0 1.0 CA D:ILE73 4.9 65.9 1.0

Sodium binding site 6 out of 6 in the Glic Mutant E35A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Glic Mutant E35A within 5.0Å range: probe atom residue distance (Å) B Occ E:Na405 b:83.0 occ:1.00 O E:ILE71 2.4 77.7 1.0 O E:PRO68 2.9 94.3 1.0 C E:ILE71 3.6 77.9 1.0 C E:PRO68 3.9 95.3 1.0 N E:ILE73 4.0 69.7 1.0 CG2 E:VAL5 4.0 0.0 1.0 O E:GLU69 4.2 94.3 1.0 CA E:TRP72 4.2 70.2 1.0 N E:TRP72 4.4 72.0 1.0 CA E:GLU69 4.4 93.1 1.0 CD1 E:ILE73 4.4 69.2 1.0 C E:GLU69 4.4 94.0 1.0 CB E:ILE73 4.4 69.1 1.0 C E:TRP72 4.5 73.8 1.0 CG1 E:ILE73 4.5 68.8 1.0 N E:GLU69 4.5 92.6 1.0 N E:ILE71 4.6 79.8 1.0 CA E:ILE71 4.7 77.3 1.0 CA E:ILE73 4.8 67.5 1.0

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