Sodium in PDB 4bdn: Crystal Structure of the GLUK2 K531A-T779G Lbd Dimer in Complex with Glutamate

The structure of Crystal Structure of the GLUK2 K531A-T779G Lbd Dimer in Complex with Glutamate, PDB code: 4bdn 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)	32.561 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.729, 100.133, 126.199, 90.00, 90.00, 90.00
R / Rfree (%)	19.75 / 24.79

The binding sites of Sodium atom in the Crystal Structure of the GLUK2 K531A-T779G Lbd Dimer in Complex with Glutamate (pdb code 4bdn). 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 GLUK2 K531A-T779G Lbd Dimer in Complex with Glutamate, PDB code: 4bdn:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the GLUK2 K531A-T779G 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-T779G Lbd Dimer in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:32.9 occ:1.00 O A:ILE527 2.4 24.8 1.0 O A:GLU524 2.4 25.0 1.0 OD1 A:ASP528 2.4 33.6 1.0 C A:ILE527 3.2 25.4 1.0 OD2 B:ASP776 3.2 43.2 1.0 OD1 B:ASP776 3.3 38.7 1.0 OE2 A:GLU524 3.3 42.4 1.0 C A:GLU524 3.4 27.0 1.0 CG A:ASP528 3.5 31.4 1.0 CG B:ASP776 3.6 37.9 1.0 N A:ASP528 3.7 26.2 1.0 CA A:ASP528 3.7 25.1 1.0 SD A:MET770 3.9 57.6 1.0 CD A:GLU524 4.0 39.2 1.0 CA A:GLU524 4.1 26.7 1.0 CG A:MET770 4.1 37.4 1.0 CG A:GLU524 4.1 33.2 1.0 CA A:ILE527 4.2 25.2 1.0 N A:ILE527 4.2 24.8 1.0 CB A:ASP528 4.2 27.7 1.0 OD2 A:ASP528 4.3 32.9 1.0 N A:LYS525 4.5 29.4 1.0 N A:VAL526 4.7 25.7 1.0 C A:LYS525 4.7 29.7 1.0 CB A:GLU524 4.7 27.4 1.0 CA A:LYS525 4.8 33.1 1.0 O A:HOH2046 4.8 24.2 1.0 C A:VAL526 4.8 26.2 1.0 CB A:MET770 4.8 30.2 1.0 O A:ARG523 5.0 20.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the GLUK2 K531A-T779G 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-T779G Lbd Dimer in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:33.3 occ:1.00 O B:GLU524 2.4 27.4 1.0 O B:ILE527 2.4 27.0 1.0 OD1 B:ASP528 2.4 37.7 1.0 C B:ILE527 3.0 24.8 1.0 OE2 B:GLU524 3.2 31.6 1.0 OD2 A:ASP776 3.2 36.6 1.0 OD1 A:ASP776 3.3 38.7 1.0 C B:GLU524 3.5 24.2 1.0 CG B:ASP528 3.6 35.5 1.0 SD B:MET770 3.6 60.4 1.0 CG A:ASP776 3.7 32.6 1.0 N B:ASP528 3.7 23.5 1.0 CA B:ASP528 3.8 27.3 1.0 N B:ILE527 3.9 26.9 1.0 CA B:ILE527 4.0 25.8 1.0 CD B:GLU524 4.0 29.3 1.0 CA B:GLU524 4.2 20.1 1.0 CG B:GLU524 4.2 24.9 1.0 CG B:MET770 4.2 26.9 1.0 CB B:ASP528 4.3 29.7 1.0 O A:HOH2091 4.3 33.7 1.0 C B:LYS525 4.5 32.7 1.0 N B:LYS525 4.5 28.2 1.0 OD2 B:ASP528 4.5 36.0 1.0 N B:VAL526 4.5 26.0 1.0 C B:VAL526 4.6 27.4 1.0 CA B:LYS525 4.7 29.9 1.0 O B:LYS525 4.7 37.9 1.0 CB B:MET770 4.8 25.4 1.0 CB B:GLU524 4.8 19.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the GLUK2 K531A-T779G 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 3 of Crystal Structure of the GLUK2 K531A-T779G Lbd Dimer in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na902 b:45.0 occ:0.82 O C:GLU524 2.4 43.2 1.0 O C:ILE527 2.4 38.2 1.0 OD1 C:ASP528 2.4 40.1 1.0 C C:ILE527 3.0 36.2 1.0 OD2 D:ASP776 3.3 69.9 1.0 OE2 C:GLU524 3.4 49.1 1.0 C C:GLU524 3.4 42.5 1.0 CG C:ASP528 3.6 37.2 1.0 N C:ASP528 3.6 35.0 1.0 N C:ILE527 3.7 39.2 1.0 OD1 D:ASP776 3.8 60.3 1.0 CA C:ASP528 3.8 34.5 1.0 CA C:ILE527 3.9 34.1 1.0 CD C:GLU524 3.9 46.6 1.0 CG D:ASP776 3.9 66.4 1.0 C C:LYS525 4.2 47.0 1.0 CA C:GLU524 4.2 35.6 1.0 C C:VAL526 4.3 42.0 1.0 N C:VAL526 4.3 40.0 1.0 CB C:ASP528 4.3 31.5 1.0 CG C:MET770 4.3 45.7 1.0 N C:LYS525 4.4 44.3 1.0 O C:LYS525 4.4 53.2 1.0 CG C:GLU524 4.5 39.2 1.0 CA C:LYS525 4.5 46.1 1.0 OE1 C:GLU524 4.5 47.6 1.0 OD2 C:ASP528 4.5 41.4 1.0 O C:HOH2028 4.8 36.7 1.0 CA C:VAL526 4.8 38.1 1.0 CE C:MET770 4.8 0.4 1.0 O C:ARG523 4.8 33.3 1.0 O C:VAL526 4.8 47.5 1.0 CB C:MET770 4.9 44.5 1.0 CB C:GLU524 5.0 33.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the GLUK2 K531A-T779G 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 4 of Crystal Structure of the GLUK2 K531A-T779G Lbd Dimer in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na902 b:31.9 occ:1.00 O D:GLU524 2.4 32.5 1.0 O D:ILE527 2.4 28.2 1.0 OD1 D:ASP528 2.4 43.5 1.0 C D:ILE527 3.1 31.3 1.0 OD1 C:ASP776 3.3 56.6 1.0 OD2 C:ASP776 3.3 55.0 1.0 OE2 D:GLU524 3.4 42.6 1.0 C D:GLU524 3.4 31.6 1.0 CG D:ASP528 3.5 42.4 1.0 CG C:ASP776 3.7 52.3 1.0 N D:ASP528 3.7 33.6 1.0 CA D:ASP528 3.7 34.5 1.0 SD D:MET770 3.8 70.6 1.0 CD D:GLU524 3.9 40.5 1.0 N D:ILE527 4.1 30.9 1.0 CG D:GLU524 4.1 31.7 1.0 CA D:ILE527 4.1 31.7 1.0 CA D:GLU524 4.1 24.7 1.0 CB D:ASP528 4.3 37.6 1.0 N D:LYS525 4.4 34.8 1.0 CG D:MET770 4.4 45.8 1.0 OD2 D:ASP528 4.5 45.0 1.0 C D:LYS525 4.6 36.0 1.0 N D:VAL526 4.6 32.5 1.0 CA D:LYS525 4.7 34.1 1.0 C D:VAL526 4.7 35.1 1.0 O C:HOH2056 4.7 34.6 1.0 OE1 D:GLU524 4.7 40.8 1.0 CB D:GLU524 4.8 22.3 1.0 CB D:MET770 5.0 45.2 1.0 O D:LYS525 5.0 38.1 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