Sodium in PDB 3s9e: Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate

The structure of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate, PDB code: 3s9e was solved by R.Venskutonyte, K.Frydenvang, M.Gajhede, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.90 / 1.60
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	67.800, 67.800, 122.430, 90.00, 90.00, 90.00
R / Rfree (%)	13.5 / 18.4

The structure of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate (pdb code 3s9e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate, PDB code: 3s9e:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na265 b:19.0 occ:1.00 O A:HOH369 2.6 45.3 1.0 O A:ARG26 2.7 20.0 1.0 O A:HOH348 2.9 38.4 1.0 O A:SER24 2.9 26.8 1.0 O A:HOH362 2.9 21.9 1.0 O A:HOH522 3.2 42.2 1.0 HA A:THR27 3.4 22.6 1.0 HB3 A:SER24 3.5 24.5 1.0 H A:SER24 3.7 22.1 1.0 HG A:LEU28 3.7 15.7 1.0 C A:ARG26 3.8 20.7 1.0 C A:SER24 3.8 21.8 1.0 H A:LEU28 4.0 16.6 1.0 O A:ASP25 4.2 29.8 1.0 CA A:THR27 4.3 18.9 1.0 C A:ASP25 4.3 27.3 1.0 CB A:SER24 4.3 20.5 1.0 N A:THR27 4.4 18.8 1.0 N A:SER24 4.4 18.5 1.0 CA A:SER24 4.4 20.0 1.0 HA A:ASP25 4.6 33.1 1.0 O A:HOH302 4.6 32.3 1.0 N A:ARG26 4.7 24.0 1.0 N A:ASP25 4.7 24.2 1.0 N A:LEU28 4.7 13.9 1.0 CA A:ASP25 4.8 27.6 1.0 CG A:LEU28 4.8 13.1 1.0 CA A:ARG26 4.9 23.6 1.0 O A:HOH528 4.9 40.6 1.0 OG A:SER24 5.0 23.4 1.0 C A:THR27 5.0 18.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na263 b:19.4 occ:1.00 O B:ARG26 2.6 19.6 1.0 O B:HOH484 2.7 39.4 1.0 O B:HOH480 2.8 42.5 1.0 O B:HOH359 2.9 20.2 1.0 O B:HOH405 2.9 36.2 1.0 O B:HOH304 2.9 43.8 1.0 O B:SER24 2.9 23.5 1.0 HB3 B:SER24 3.4 21.4 1.0 HA B:THR27 3.4 19.7 1.0 C B:ARG26 3.7 20.9 1.0 HG B:LEU28 3.7 14.2 1.0 H B:SER24 3.8 20.0 1.0 C B:SER24 3.8 19.0 1.0 H B:LEU28 4.0 16.3 1.0 CA B:THR27 4.3 16.5 1.0 CB B:SER24 4.3 17.9 1.0 O B:ASP25 4.4 30.3 1.0 N B:THR27 4.4 19.1 1.0 C B:ASP25 4.4 26.8 1.0 N B:SER24 4.4 16.8 1.0 CA B:SER24 4.4 17.2 1.0 HA B:ASP25 4.6 32.0 1.0 O B:HOH351 4.6 37.4 1.0 N B:ARG26 4.6 24.5 1.0 N B:ASP25 4.7 21.7 1.0 N B:LEU28 4.7 13.6 1.0 CG B:LEU28 4.8 11.9 1.0 CA B:ASP25 4.8 26.7 1.0 CA B:ARG26 4.8 24.1 1.0 O B:HOH747 4.9 37.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na264 b:10.3 occ:1.00 O B:ASN5 2.7 17.2 1.0 OG B:SER52 2.8 13.4 1.0 O B:HOH265 3.0 12.6 1.0 O B:HOH668 3.1 25.9 1.0 HG B:SER52 3.4 16.0 1.0 H B:SER52 3.5 12.3 1.0 C B:ASN5 3.9 18.6 1.0 HB3 B:ASN5 3.9 30.9 1.0 HB3 B:SER52 3.9 14.9 1.0 CB B:SER52 4.0 12.5 1.0 O B:HOH394 4.1 25.1 1.0 N B:SER52 4.2 10.3 1.0 HA B:PHE51 4.3 11.2 1.0 HA B:ASN5 4.4 29.2 1.0 HA B:SER7 4.4 16.0 1.0 CA B:ASN5 4.6 24.4 1.0 C B:ARG6 4.6 14.9 1.0 O B:ARG6 4.6 14.0 1.0 OG B:SER7 4.6 16.3 1.0 CA B:SER52 4.7 10.3 1.0 CB B:ASN5 4.7 25.9 1.0 N B:SER7 4.7 12.8 1.0 HB2 B:SER52 4.8 14.9 1.0 HA B:ARG6 4.8 19.2 1.0 N B:ARG6 4.9 16.3 1.0

R.Venskutonyte, K.Frydenvang, M.Gajhede, L.Bunch, D.S.Pickering, J.S.Kastrup. Binding Site and Interlobe Interactions of the Ionotropic Glutamate Receptor GLUK3 Ligand Binding Domain Revealed By High Resolution Crystal Structure in Complex with (S)-Glutamate. J.Struct.Biol. V. 176 307 2011.
ISSN: ISSN 1047-8477
PubMed: 21907808
DOI: 10.1016/J.JSB.2011.08.014