Sodium in PDB 4bdl: Crystal Structure of the GLUK2 K531A Lbd Dimer in Complex with Glutamate

The structure of Crystal Structure of the GLUK2 K531A Lbd Dimer in Complex with Glutamate, PDB code: 4bdl was solved by N.Nayeem, O.Mayans, T.Green, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.924 / 1.75
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.568, 106.611, 113.904, 90.00, 90.00, 90.00
R / Rfree (%)	16.93 / 20.16

The binding sites of Sodium atom in the Crystal Structure of the GLUK2 K531A Lbd Dimer in Complex with Glutamate (pdb code 4bdl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the GLUK2 K531A Lbd Dimer in Complex with Glutamate, PDB code: 4bdl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the GLUK2 K531A Lbd Dimer in Complex with 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 GLUK2 K531A Lbd Dimer in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:19.5 occ:1.00 O A:GLU524 2.3 13.2 1.0 O A:ILE527 2.4 14.9 1.0 OD1 A:ASP528 2.4 21.2 1.0 OE2 A:GLU524 2.4 23.4 1.0 OD2 B:ASP776 2.7 30.5 1.0 CE A:MET770 3.0 18.9 1.0 OD1 B:ASP776 3.2 30.0 1.0 CD A:GLU524 3.2 23.9 1.0 C A:ILE527 3.2 13.6 1.0 CG B:ASP776 3.3 32.4 1.0 C A:GLU524 3.4 13.0 1.0 CG A:ASP528 3.5 21.9 1.0 CA A:ASP528 3.7 15.3 1.0 CG A:GLU524 3.7 19.1 1.0 N A:ASP528 3.8 12.5 1.0 CA A:GLU524 4.0 12.7 1.0 O A:HOH2130 4.1 39.5 1.0 OE1 A:GLU524 4.1 24.6 1.0 CB A:ASP528 4.1 14.8 1.0 N A:ILE527 4.2 14.2 1.0 CA A:ILE527 4.3 10.8 1.0 CB A:GLU524 4.4 11.4 1.0 SD A:MET770 4.5 48.4 1.0 CG A:MET770 4.5 34.3 1.0 N A:LYS525 4.5 11.3 1.0 O A:HOH2124 4.5 26.8 1.0 OD2 A:ASP528 4.6 24.6 1.0 C A:LYS525 4.7 14.6 1.0 CB B:ASP776 4.7 24.6 1.0 N A:VAL526 4.8 12.6 1.0 O B:HOH2222 4.8 27.5 1.0 CA A:LYS525 4.8 11.8 1.0 C A:VAL526 4.9 14.8 1.0 C A:ASP528 4.9 18.0 1.0 NH2 B:ARG775 5.0 43.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the GLUK2 K531A Lbd Dimer in Complex with 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 GLUK2 K531A Lbd Dimer in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:25.1 occ:1.00 O B:GLU524 2.4 18.5 1.0 O B:ILE527 2.4 16.7 1.0 OE2 B:GLU524 2.4 26.4 1.0 OD1 B:ASP528 2.4 25.7 1.0 OD2 A:ASP776 2.8 33.0 1.0 C B:ILE527 3.2 19.8 1.0 CD B:GLU524 3.2 26.4 1.0 OD1 A:ASP776 3.3 29.4 1.0 CG A:ASP776 3.4 26.5 1.0 C B:GLU524 3.4 19.5 1.0 CG B:ASP528 3.6 24.8 1.0 CA B:ASP528 3.7 20.0 1.0 N B:ASP528 3.8 16.6 1.0 CG B:GLU524 3.8 23.9 1.0 SD B:MET770 3.8 60.4 1.0 CA B:GLU524 4.0 18.2 1.0 CG B:MET770 4.0 35.7 1.0 OE1 B:GLU524 4.1 22.9 1.0 CB B:ASP528 4.2 20.9 1.0 N B:ILE527 4.2 15.4 1.0 CA B:ILE527 4.3 14.8 1.0 CB B:GLU524 4.5 17.6 1.0 N B:LYS525 4.5 13.4 1.0 O A:HOH2234 4.6 37.3 1.0 OD2 B:ASP528 4.6 26.9 1.0 O A:HOH2233 4.6 32.1 1.0 C B:LYS525 4.7 23.5 1.0 N B:VAL526 4.8 21.2 1.0 CA B:LYS525 4.8 16.1 1.0 CB A:ASP776 4.9 21.9 1.0 C B:VAL526 4.9 20.8 1.0 C B:ASP528 4.9 18.8 1.0

N.Nayeem, O.Mayans, T.Green. Correlating Efficacy and Desensitization with GLUK2 Ligand- Binding Domain Movements. Open Biol. V. 3 0051 2013.
ISSN: ISSN 2046-2441
PubMed: 23720540
DOI: 10.1098/RSOB.130051