Sodium in PDB 3g3f: Crystal Structure of the GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution

The structure of Crystal Structure of the GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution, PDB code: 3g3f was solved by C.Chaudhry, M.L.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.71 / 1.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.185, 114.153, 52.364, 90.00, 115.31, 90.00
R / Rfree (%)	15.2 / 17.5

The structure of Crystal Structure of the GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution (pdb code 3g3f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution, PDB code: 3g3f:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution


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 GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na262 b:21.7 occ:0.90 O A:HOH378 2.3 24.1 1.0 O A:GLU97 2.3 18.5 1.0 O A:ILE100 2.4 14.5 1.0 OD1 A:ASP101 2.4 22.9 1.0 HE1 A:MET223 2.5 26.1 0.5 OE2 A:GLU97 2.6 26.7 1.0 HA A:ASP101 2.8 16.2 1.0 HE2 A:MET223 3.0 26.1 0.5 HG3 A:GLU97 3.0 30.9 1.0 HE1 A:MET223 3.1 34.9 0.5 CE A:MET223 3.1 21.8 0.5 HA A:GLU97 3.3 17.5 1.0 C A:GLU97 3.3 15.7 1.0 HE3 A:MET223 3.3 26.1 0.5 C A:ILE100 3.4 13.7 1.0 CD A:GLU97 3.5 22.5 1.0 SD A:MET223 3.5 32.4 0.5 CG A:ASP101 3.6 21.0 1.0 O A:HOH567 3.6 15.6 0.6 CA A:ASP101 3.6 13.5 1.0 CE A:MET223 3.7 29.1 0.5 CG A:GLU97 3.7 25.7 1.0 CA A:GLU97 3.7 14.6 1.0 N A:ASP101 3.9 13.2 1.0 HE2 A:MET223 3.9 34.9 0.5 O B:HOH395 4.0 20.4 1.0 HH22 A:ARG228 4.0 33.7 0.4 HH21 A:ARG228 4.1 33.7 0.4 HD11 B:ILE233 4.2 27.4 1.0 NH2 A:ARG228 4.2 28.1 0.4 HG3 A:MET223 4.2 29.8 0.5 CB A:ASP101 4.2 16.7 1.0 CB A:GLU97 4.2 18.1 1.0 H A:ILE100 4.3 16.2 1.0 O A:HOH563 4.4 34.9 1.0 N A:LYS98 4.4 16.5 1.0 HA A:LYS98 4.5 24.3 1.0 N A:ILE100 4.5 13.5 1.0 HE3 A:MET223 4.5 34.9 0.5 HG2 A:GLU97 4.5 30.9 1.0 CA A:ILE100 4.6 14.8 1.0 H A:PHE102 4.6 17.3 1.0 OD2 A:ASP101 4.6 21.4 1.0 HB3 A:ASP101 4.7 20.1 1.0 H A:ASP101 4.7 15.9 1.0 OE1 A:GLU97 4.7 22.0 1.0 SD A:MET223 4.7 31.3 0.5 O B:HOH578 4.8 30.1 0.5 H A:VAL99 4.8 20.2 1.0 C A:ASP101 4.8 14.9 1.0 HB3 A:GLU97 4.8 21.7 1.0 CA A:LYS98 4.8 20.2 1.0 C A:LYS98 4.9 19.5 1.0 N A:VAL99 4.9 16.9 1.0 HD2 A:PHE102 4.9 18.8 1.0 CZ A:ARG228 4.9 25.3 0.4 CG A:MET223 4.9 24.9 0.5 HA A:MET223 4.9 22.1 0.5 HA A:MET223 4.9 22.3 0.5 HB2 A:GLU97 4.9 21.7 1.0 O A:ARG96 4.9 14.0 1.0 HA A:ILE100 4.9 17.8 1.0 HB2 A:ASP101 4.9 20.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution


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 GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na261 b:19.4 occ:0.80 O B:HOH469 2.3 23.9 1.0 O B:GLU97 2.3 14.9 1.0 O B:ILE100 2.3 12.2 1.0 OD1 B:ASP101 2.3 19.9 1.0 HE2 B:MET223 2.4 22.4 0.7 OE2 B:GLU97 2.6 23.0 1.0 HA B:ASP101 2.7 15.3 0.7 HA B:ASP101 2.8 15.5 0.3 HE1 B:MET223 3.0 24.3 0.3 CE B:MET223 3.0 18.7 0.7 HE1 B:MET223 3.1 22.4 0.7 HG3 B:GLU97 3.1 28.4 1.0 HE3 B:MET223 3.2 22.4 0.7 HA B:GLU97 3.3 15.7 1.0 C B:ILE100 3.3 11.2 1.0 C B:GLU97 3.3 14.1 1.0 CG B:ASP101 3.5 17.0 1.0 CD B:GLU97 3.6 24.8 1.0 CA B:ASP101 3.6 12.7 0.7 O B:HOH454 3.6 12.6 0.5 CE B:MET223 3.6 20.3 0.3 CA B:ASP101 3.6 12.9 0.3 SD B:MET223 3.7 25.1 0.3 CG B:GLU97 3.7 23.7 1.0 CA B:GLU97 3.8 13.1 1.0 HE2 B:MET223 3.8 24.3 0.3 N B:ASP101 3.8 11.3 0.7 N B:ASP101 3.9 12.9 0.3 O A:HOH328 4.0 22.7 1.0 O A:HOH581 4.1 42.0 1.0 CB B:ASP101 4.1 13.5 1.0 HH21 B:ARG228 4.1 28.4 0.3 H B:ILE100 4.2 13.1 1.0 HH22 B:ARG228 4.2 28.4 0.3 NH2 B:ARG228 4.3 23.7 0.3 HD11 A:ILE233 4.3 24.2 1.0 CB B:GLU97 4.3 15.9 1.0 HG3 B:MET223 4.4 24.3 0.7 H B:PHE102 4.4 14.6 1.0 HE3 B:MET223 4.4 24.3 0.3 N B:LYS98 4.5 12.8 1.0 N B:ILE100 4.5 10.9 1.0 OD2 B:ASP101 4.5 18.8 1.0 O A:HOH452 4.5 31.9 1.0 CA B:ILE100 4.5 11.8 1.0 HA B:LYS98 4.5 18.5 1.0 HG2 B:GLU97 4.6 28.4 1.0 SD B:MET223 4.6 32.4 0.7 HB3 B:ASP101 4.6 16.2 0.7 HB3 B:ASP101 4.6 16.2 0.3 H B:ASP101 4.6 13.5 0.7 H B:ASP101 4.7 15.5 0.3 OE1 B:GLU97 4.7 21.5 1.0 C B:ASP101 4.7 11.6 0.7 HB2 B:ASP101 4.8 16.2 0.3 HB2 B:ASP101 4.8 16.2 0.7 CA B:LYS98 4.9 15.4 1.0 O A:HOH579 4.9 30.4 0.6 C B:LYS98 4.9 15.0 1.0 HA B:ILE100 4.9 14.2 1.0 HA B:MET223 4.9 20.0 0.3 C B:ASP101 4.9 14.3 0.3 HB3 B:GLU97 4.9 19.1 1.0 HA B:MET223 4.9 18.5 0.7 H B:VAL99 4.9 16.2 1.0 O B:ARG96 4.9 11.1 1.0 N B:VAL99 4.9 13.5 1.0 CZ B:ARG228 4.9 27.3 0.3 HB2 B:GLU97 5.0 19.1 1.0 HD2 B:PHE102 5.0 16.6 1.0 N B:PHE102 5.0 12.1 1.0 CG B:MET223 5.0 20.3 0.7

Sodium binding site 3 out of 4 in the Crystal Structure of the GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution


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 GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na262 b:31.6 occ:0.85 O B:HOH426 2.4 25.8 1.0 O B:HOH479 2.4 25.9 1.0 O B:SER22 3.1 28.9 1.0 H B:SER22 3.2 23.5 0.7 H B:SER22 3.2 23.5 0.3 O B:HOH483 3.7 25.8 1.0 N B:SER22 4.0 19.6 1.0 HA B:LYS21 4.1 21.2 1.0 C B:SER22 4.2 26.5 1.0 OG B:SER22 4.2 23.0 0.7 HB3 B:SER22 4.2 29.8 0.3 CA B:SER22 4.6 23.6 0.3 O B:LYS20 4.6 17.4 1.0 CA B:SER22 4.6 21.6 0.7 HG B:SER22 4.7 27.6 0.7 CB B:SER22 4.9 24.8 0.3 O B:HOH532 5.0 32.8 1.0 CA B:LYS21 5.0 17.7 1.0 C B:LYS21 5.0 21.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the GLUR6 Ligand Binding Domain Dimer with Glutamate and Nacl at 1.38 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na263 b:28.8 occ:0.67 O B:HOH459 2.4 36.0 1.0 HG12 B:ILE11 2.9 15.0 1.0 O B:LEU12 2.9 13.4 1.0 O B:HOH341 3.0 16.6 1.0 O B:HOH416 3.0 32.9 1.0 HB2 B:LEU12 3.0 14.7 1.0 O B:HOH364 3.1 33.0 1.0 H B:LEU12 3.4 12.5 1.0 O B:HOH467 3.6 22.9 0.5 HG13 B:ILE11 3.6 15.0 1.0 CG1 B:ILE11 3.6 12.5 1.0 HD11 B:ILE11 3.8 20.7 1.0 N B:LEU12 3.8 10.4 1.0 C B:LEU12 3.8 11.4 1.0 CB B:LEU12 3.9 12.2 1.0 CA B:LEU12 4.1 10.6 1.0 HB3 B:SER173 4.1 24.1 1.0 CD1 B:ILE11 4.2 17.2 1.0 HB2 B:SER173 4.2 24.1 1.0 HB3 B:LEU12 4.4 14.7 1.0 HD13 B:ILE11 4.5 20.7 1.0 HD12 B:LEU12 4.6 19.7 1.0 O B:HOH520 4.7 25.2 0.7 CB B:SER173 4.7 20.1 1.0 C B:ILE11 4.7 11.2 1.0 HG B:LEU12 4.8 14.5 1.0 CB B:ILE11 4.9 9.9 1.0 CG B:LEU12 4.9 12.1 1.0 HB2 B:GLU13 4.9 18.0 0.5 O B:GLY59 5.0 17.6 1.0 HA B:ILE11 5.0 13.2 1.0

C.Chaudhry, M.C.Weston, P.Schuck, C.Rosenmund, M.L.Mayer. Stability of Ligand-Binding Domain Dimer Assembly Controls Kainate Receptor Desensitization. Embo J. V. 28 1518 2009.
ISSN: ISSN 0261-4189
PubMed: 19339989
DOI: 10.1038/EMBOJ.2009.86