Sodium in PDB 4lmk: Glic Liganded-Closed-Channel Conformation, Mutant Y27'A

The structure of Glic Liganded-Closed-Channel Conformation, Mutant Y27'A, PDB code: 4lmk was solved by C.Grosman, G.Gonzalez-Gutierrez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.76 / 3.22
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.990, 134.280, 159.940, 90.00, 102.06, 90.00
R / Rfree (%)	21.1 / 23.8

The structure of Glic Liganded-Closed-Channel Conformation, Mutant Y27'A also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Glic Liganded-Closed-Channel Conformation, Mutant Y27'A (pdb code 4lmk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Glic Liganded-Closed-Channel Conformation, Mutant Y27'A, PDB code: 4lmk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Glic Liganded-Closed-Channel Conformation, Mutant Y27'A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glic Liganded-Closed-Channel Conformation, Mutant Y27'A within 5.0Å range: probe atom residue distance (Å) B Occ E:Na402 b:38.2 occ:1.00 OE1 E:GLU242 3.2 70.9 1.0 OE2 E:GLU242 3.4 83.3 1.0 O A:ILE239 3.4 29.5 1.0 OE2 A:GLU242 3.6 71.2 1.0 CD E:GLU242 3.7 79.8 1.0 OG1 A:THR243 3.8 64.9 1.0 CB A:GLU242 4.0 56.3 1.0 C12 E:LMT401 4.4 51.7 1.0 N A:THR243 4.5 49.1 1.0 CD A:GLU242 4.5 77.6 1.0 C A:ILE239 4.6 21.6 1.0 CG A:GLU242 4.7 66.2 1.0 N A:GLU242 4.7 46.0 1.0 O A:LEU240 4.8 47.6 1.0 CA A:GLU242 4.8 40.9 1.0 C10 E:LMT401 4.8 44.0 1.0 CG2 A:ILE239 4.9 11.7 1.0 C A:GLU242 5.0 46.9 1.0

Sodium binding site 2 out of 5 in the Glic Liganded-Closed-Channel Conformation, Mutant Y27'A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Glic Liganded-Closed-Channel Conformation, Mutant Y27'A within 5.0Å range: probe atom residue distance (Å) B Occ E:Na404 b:56.6 occ:1.00 OE2 E:GLU242 3.3 83.3 1.0 OE2 D:GLU242 3.8 67.7 1.0 O E:ILE239 3.9 25.4 1.0 OE1 D:GLU242 4.2 65.5 1.0 C12 E:LMT401 4.2 51.7 1.0 C10 E:LMT401 4.3 44.0 1.0 CD E:GLU242 4.3 79.8 1.0 CB E:GLU242 4.3 55.5 1.0 CD D:GLU242 4.4 74.5 1.0 OG1 E:THR243 4.6 63.1 1.0 NA D:NA401 4.8 35.7 1.0 C11 E:LMT401 4.8 48.8 1.0 CG2 E:ILE239 4.8 13.4 1.0 CG E:GLU242 4.8 65.1 1.0 C E:ILE239 5.0 20.6 1.0

Sodium binding site 3 out of 5 in the Glic Liganded-Closed-Channel Conformation, Mutant Y27'A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Glic Liganded-Closed-Channel Conformation, Mutant Y27'A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:47.9 occ:1.00 OE2 B:GLU242 3.3 74.6 1.0 O B:ILE239 3.5 27.9 1.0 OE1 A:GLU242 3.8 78.3 1.0 OE2 A:GLU242 3.8 71.2 1.0 CB B:GLU242 3.9 54.3 1.0 C11 E:LMT401 4.1 48.8 1.0 CD B:GLU242 4.2 78.1 1.0 OG1 B:THR243 4.2 61.2 1.0 CD A:GLU242 4.2 77.6 1.0 C12 E:LMT401 4.4 51.7 1.0 CG B:GLU242 4.6 68.0 1.0 C B:ILE239 4.7 21.9 1.0 N B:THR243 4.7 44.4 1.0 CG2 B:ILE239 4.8 15.5 1.0 CA B:GLU242 4.9 41.1 1.0 N B:GLU242 5.0 42.1 1.0 NA B:NA402 5.0 50.4 1.0

Sodium binding site 4 out of 5 in the Glic Liganded-Closed-Channel Conformation, Mutant Y27'A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Glic Liganded-Closed-Channel Conformation, Mutant Y27'A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:50.4 occ:1.00 OE2 B:GLU242 3.4 74.6 1.0 OE2 C:GLU242 3.6 74.7 1.0 OE1 B:GLU242 3.7 71.9 1.0 O C:ILE239 3.7 29.0 1.0 CD B:GLU242 3.9 78.1 1.0 C11 E:LMT401 4.1 48.8 1.0 OG1 C:THR243 4.2 67.6 1.0 CB C:GLU242 4.3 56.1 1.0 CD C:GLU242 4.6 78.8 1.0 C C:ILE239 4.8 21.5 1.0 CG2 C:ILE239 4.9 15.7 1.0 C12 E:LMT401 4.9 51.7 1.0 CG C:GLU242 5.0 68.5 1.0 N C:THR243 5.0 48.3 1.0 NA B:NA401 5.0 47.9 1.0

Sodium binding site 5 out of 5 in the Glic Liganded-Closed-Channel Conformation, Mutant Y27'A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Glic Liganded-Closed-Channel Conformation, Mutant Y27'A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:35.7 occ:1.00 OE2 D:GLU242 3.4 67.7 1.0 OE2 C:GLU242 3.7 74.7 1.0 O D:ILE239 3.8 37.0 1.0 OE1 C:GLU242 4.0 74.0 1.0 CD C:GLU242 4.3 78.8 1.0 C11 E:LMT401 4.4 48.8 1.0 CD D:GLU242 4.5 74.5 1.0 CG2 D:ILE239 4.5 12.8 1.0 CB D:GLU242 4.5 54.1 1.0 C10 E:LMT401 4.6 44.0 1.0 C12 E:LMT401 4.7 51.7 1.0 NA E:NA404 4.8 56.6 1.0 C D:ILE239 4.9 21.8 1.0 OG1 D:THR243 4.9 63.0 1.0

G.Gonzalez-Gutierrez, L.G.Cuello, S.K.Nair, C.Grosman. Gating of the Proton-Gated Ion Channel From Gloeobacter Violaceus at pH 4 As Revealed By X-Ray Crystallography. Proc.Natl.Acad.Sci.Usa V. 110 18716 2013.
ISSN: ISSN 0027-8424
PubMed: 24167270
DOI: 10.1073/PNAS.1313156110