Sodium in PDB 4lmj: Glic Liganded-Closed-Channel Conformation, Mutant T25'A

The structure of Glic Liganded-Closed-Channel Conformation, Mutant T25'A, PDB code: 4lmj 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)	49.04 / 3.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	181.120, 134.320, 159.890, 90.00, 101.96, 90.00
R / Rfree (%)	22.7 / 25.5

The structure of Glic Liganded-Closed-Channel Conformation, Mutant T25'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 T25'A (pdb code 4lmj). 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 T25'A, PDB code: 4lmj:
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 T25'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 T25'A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:55.7 occ:1.00 OE1 B:GLU242 3.3 84.7 1.0 OE1 C:GLU242 3.4 88.8 1.0 OE2 B:GLU242 3.5 69.2 1.0 O C:ILE239 3.7 48.2 1.0 CD B:GLU242 3.8 78.9 1.0 OG1 C:THR243 4.0 83.4 1.0 CB C:GLU242 4.1 61.6 1.0 CD C:GLU242 4.5 83.4 1.0 N C:THR243 4.8 62.1 1.0 C C:ILE239 4.8 42.7 1.0 C11 E:LMT402 4.9 56.3 1.0 CG C:GLU242 4.9 68.9 1.0 CG2 C:ILE239 4.9 39.4 1.0

Sodium binding site 2 out of 5 in the Glic Liganded-Closed-Channel Conformation, Mutant T25'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 T25'A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:63.2 occ:1.00 OE1 B:GLU242 3.1 84.7 1.0 O B:ILE239 3.4 53.2 1.0 OE2 A:GLU242 3.5 84.0 1.0 OE1 A:GLU242 3.6 76.9 1.0 CB B:GLU242 3.9 63.3 1.0 CD A:GLU242 4.0 77.7 1.0 OG1 B:THR243 4.1 72.0 1.0 CD B:GLU242 4.3 78.9 1.0 C11 E:LMT402 4.3 56.3 1.0 C B:ILE239 4.6 47.2 1.0 CG B:GLU242 4.7 71.8 1.0 CG2 B:ILE239 4.7 41.1 1.0 N B:THR243 4.7 65.8 1.0 C12 E:LMT402 4.8 60.1 1.0 CA B:GLU242 4.9 59.9 1.0 N B:GLU242 4.9 60.4 1.0

Sodium binding site 3 out of 5 in the Glic Liganded-Closed-Channel Conformation, Mutant T25'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 T25'A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:63.7 occ:1.00 OE1 D:GLU242 3.3 79.2 1.0 OE1 C:GLU242 3.4 88.8 1.0 O D:ILE239 3.8 57.4 1.0 OE2 C:GLU242 3.9 75.6 1.0 C12 E:LMT402 4.1 60.1 1.0 CD C:GLU242 4.1 83.4 1.0 CG2 D:ILE239 4.3 38.0 1.0 C10 E:LMT402 4.5 53.6 1.0 C11 E:LMT402 4.5 56.3 1.0 CD D:GLU242 4.5 75.3 1.0 NA D:NA401 4.6 50.4 1.0 CB D:GLU242 4.7 62.8 1.0 C D:ILE239 4.9 48.1 1.0 C9 E:LMT402 4.9 43.4 1.0

Sodium binding site 4 out of 5 in the Glic Liganded-Closed-Channel Conformation, Mutant T25'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 T25'A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:56.8 occ:1.00 OE1 A:GLU242 3.1 76.9 1.0 OE2 E:GLU242 3.4 76.3 1.0 O A:ILE239 3.5 51.2 1.0 OE1 E:GLU242 3.6 83.6 1.0 CB A:GLU242 3.8 63.0 1.0 CD E:GLU242 4.0 78.2 1.0 OG1 A:THR243 4.0 64.1 1.0 CD A:GLU242 4.1 77.7 1.0 C12 E:LMT402 4.3 60.1 1.0 CG A:GLU242 4.5 65.6 1.0 N A:THR243 4.6 67.1 1.0 C11 E:LMT402 4.6 56.3 1.0 C A:ILE239 4.7 45.7 1.0 CA A:GLU242 4.8 60.7 1.0 CG2 A:ILE239 4.8 35.4 1.0 N A:GLU242 4.9 63.2 1.0 C A:GLU242 5.0 64.1 1.0

Sodium binding site 5 out of 5 in the Glic Liganded-Closed-Channel Conformation, Mutant T25'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 T25'A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:50.4 occ:1.00 OE1 E:GLU242 3.3 83.6 1.0 OE1 D:GLU242 3.3 79.2 1.0 OE2 D:GLU242 3.5 76.0 1.0 O E:ILE239 3.6 53.1 1.0 CD D:GLU242 3.9 75.3 1.0 C12 E:LMT402 4.0 60.1 1.0 CB E:GLU242 4.3 67.0 1.0 OG1 E:THR243 4.5 71.9 1.0 C10 E:LMT402 4.5 53.6 1.0 CD E:GLU242 4.5 78.2 1.0 CG2 E:ILE239 4.6 36.1 1.0 NA C:NA401 4.6 63.7 1.0 C E:ILE239 4.7 46.9 1.0 C11 E:LMT402 4.9 56.3 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