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

The structure of Crystal Structure of the GLUK2 K531A-T779G Lbd Dimer in Complex with Kainate, PDB code: 4bdo 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)	40.785 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.838, 99.819, 124.986, 90.00, 90.00, 90.00
R / Rfree (%)	19.13 / 24.07

The binding sites of Sodium atom in the Crystal Structure of the GLUK2 K531A-T779G Lbd Dimer in Complex with Kainate (pdb code 4bdo). 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 Kainate, PDB code: 4bdo:
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 Kainate


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 Kainate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:30.0 occ:1.00 O A:ILE527 2.4 47.2 1.0 O A:GLU524 2.4 42.4 1.0 OD1 A:ASP528 2.4 50.8 1.0 OE2 A:GLU524 2.4 38.3 1.0 OD1 B:ASP776 2.9 49.8 1.0 CD A:GLU524 3.1 41.6 1.0 OD2 B:ASP776 3.1 55.2 1.0 C A:ILE527 3.2 44.2 1.0 CG B:ASP776 3.4 50.0 1.0 CG A:GLU524 3.4 43.0 1.0 C A:GLU524 3.5 41.1 1.0 CG A:ASP528 3.5 45.5 1.0 CA A:ASP528 3.6 41.4 1.0 N A:ASP528 3.7 42.7 1.0 CA A:GLU524 4.0 37.1 1.0 OE1 A:GLU524 4.1 49.0 1.0 CB A:ASP528 4.2 40.0 1.0 O A:HOH2019 4.2 34.7 1.0 CB A:GLU524 4.3 37.7 1.0 N A:ILE527 4.4 40.3 1.0 CA A:ILE527 4.4 40.0 1.0 OD2 A:ASP528 4.5 47.4 1.0 N A:LYS525 4.6 40.6 1.0 C A:LYS525 4.8 43.5 1.0 N A:VAL526 4.8 32.6 1.0 CD1 B:ILE780 4.8 31.4 1.0 C A:ASP528 4.9 47.4 1.0 CB B:ASP776 4.9 46.4 1.0 CA A:LYS525 4.9 46.4 1.0 N A:PHE529 5.0 43.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the GLUK2 K531A-T779G Lbd Dimer in Complex with Kainate


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 Kainate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:27.6 occ:1.00 O B:ILE527 2.4 37.8 1.0 O B:GLU524 2.4 34.7 1.0 OD1 B:ASP528 2.4 57.0 1.0 OE2 B:GLU524 2.4 51.5 1.0 OD1 A:ASP776 2.9 47.6 1.0 OD2 A:ASP776 3.1 49.4 1.0 C B:ILE527 3.1 37.2 1.0 CG A:ASP776 3.4 45.5 1.0 CD B:GLU524 3.4 44.2 1.0 C B:GLU524 3.5 33.6 1.0 CG B:ASP528 3.6 52.5 1.0 CA B:ASP528 3.7 38.3 1.0 N B:ASP528 3.7 37.8 1.0 N B:ILE527 4.1 35.0 1.0 CG B:GLU524 4.1 31.8 1.0 CA B:ILE527 4.1 35.1 1.0 CA B:GLU524 4.1 25.3 1.0 CB B:ASP528 4.3 45.4 1.0 OE1 B:GLU524 4.4 41.9 1.0 C B:LYS525 4.4 47.7 1.0 SD B:MET770 4.5 82.0 1.0 N B:LYS525 4.5 37.6 1.0 OD2 B:ASP528 4.5 50.2 1.0 N B:VAL526 4.5 46.0 1.0 O A:HOH2043 4.6 38.5 1.0 CA B:LYS525 4.6 41.1 1.0 O B:LYS525 4.7 53.1 1.0 C B:VAL526 4.7 43.4 1.0 CB B:GLU524 4.7 24.4 1.0 CD1 A:ILE780 4.8 26.3 1.0 CB A:ASP776 4.9 36.2 1.0 CG B:MET770 5.0 50.4 1.0 C B:ASP528 5.0 39.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the GLUK2 K531A-T779G Lbd Dimer in Complex with Kainate


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 Kainate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na902 b:19.2 occ:1.00 O C:GLU524 2.4 37.2 1.0 O C:ILE527 2.4 44.8 1.0 OE2 C:GLU524 2.4 42.6 1.0 OD1 C:ASP528 2.4 37.4 1.0 OD1 D:ASP776 2.8 53.9 1.0 OD2 D:ASP776 3.0 62.5 1.0 CG D:ASP776 3.3 56.2 1.0 CD C:GLU524 3.3 45.6 1.0 C C:ILE527 3.3 41.1 1.0 C C:GLU524 3.5 37.6 1.0 CG C:ASP528 3.6 34.8 1.0 CA C:ASP528 3.8 41.1 1.0 CG C:GLU524 3.8 42.5 1.0 N C:ASP528 3.9 39.9 1.0 CA C:GLU524 4.1 36.7 1.0 O C:HOH2017 4.3 31.6 1.0 OE1 C:GLU524 4.3 50.1 1.0 CB C:ASP528 4.3 38.7 1.0 CG C:MET770 4.4 48.3 1.0 N C:ILE527 4.4 40.1 1.0 CA C:ILE527 4.5 38.6 1.0 OD2 C:ASP528 4.5 35.2 1.0 N C:LYS525 4.6 39.8 1.0 CB C:GLU524 4.6 37.7 1.0 C C:LYS525 4.6 37.5 1.0 CB D:ASP776 4.8 50.3 1.0 CA C:LYS525 4.8 39.9 1.0 O C:LYS525 4.8 35.7 1.0 N C:VAL526 4.8 34.5 1.0 SD C:MET770 5.0 0.8 1.0 C C:ASP528 5.0 39.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the GLUK2 K531A-T779G Lbd Dimer in Complex with Kainate


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 Kainate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na902 b:26.7 occ:1.00 O D:ILE527 2.4 39.2 1.0 O D:GLU524 2.4 47.8 1.0 OD1 D:ASP528 2.4 45.6 1.0 OE2 D:GLU524 2.4 39.3 1.0 OD2 C:ASP776 3.0 47.4 1.0 OD1 C:ASP776 3.0 49.9 1.0 C D:ILE527 3.2 38.7 1.0 C D:GLU524 3.3 39.0 1.0 CG C:ASP776 3.3 46.7 1.0 CD D:GLU524 3.5 39.3 1.0 CG D:ASP528 3.6 44.8 1.0 CA D:ASP528 3.8 38.5 1.0 N D:ASP528 3.8 38.2 1.0 CG D:GLU524 3.9 36.0 1.0 CA D:GLU524 4.0 30.3 1.0 N D:LYS525 4.2 39.8 1.0 N D:ILE527 4.2 35.4 1.0 CA D:ILE527 4.3 37.4 1.0 CB D:ASP528 4.3 39.5 1.0 O D:HOH2009 4.3 42.7 1.0 CA D:LYS525 4.4 43.6 1.0 C D:LYS525 4.4 45.3 1.0 OE1 D:GLU524 4.5 33.8 1.0 OD2 D:ASP528 4.5 45.6 1.0 CB D:GLU524 4.5 32.3 1.0 N D:VAL526 4.6 37.0 1.0 SD D:MET770 4.7 99.7 1.0 O C:HOH2035 4.7 33.4 1.0 O D:LYS525 4.8 50.5 1.0 CB C:ASP776 4.8 40.1 1.0 C D:VAL526 4.9 37.7 1.0 O D:ARG523 5.0 34.2 1.0 CD1 C:ILE780 5.0 25.7 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