Sodium in PDB 5dtb: Crystal Structure of the Drosophila CG3822 KAIR1D Ligand Binding Domain Complex with Glutamate

The structure of Crystal Structure of the Drosophila CG3822 KAIR1D Ligand Binding Domain Complex with Glutamate, PDB code: 5dtb was solved by P.Dharkar, M.L.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.80 / 1.84
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.704, 87.704, 183.341, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.4

The binding sites of Sodium atom in the Crystal Structure of the Drosophila CG3822 KAIR1D Ligand Binding Domain Complex with Glutamate (pdb code 5dtb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Drosophila CG3822 KAIR1D Ligand Binding Domain Complex with Glutamate, PDB code: 5dtb:

Sodium binding site 1 out of 1 in the Crystal Structure of the Drosophila CG3822 KAIR1D Ligand Binding Domain 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 Drosophila CG3822 KAIR1D Ligand Binding Domain Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:25.7 occ:1.00 O B:GLU101 2.2 26.0 1.0 O B:VAL104 2.2 26.1 1.0 OD1 B:ASP105 2.4 29.8 1.0 O B:HOH593 2.4 32.1 1.0 OE2 B:GLU101 2.5 27.9 1.0 O B:HOH589 2.6 41.3 1.0 HA B:ASP105 2.9 27.6 1.0 C B:VAL104 3.1 27.2 1.0 HG3 B:GLU101 3.2 35.4 1.0 CD B:GLU101 3.2 30.6 1.0 C B:GLU101 3.3 25.3 1.0 HA B:GLU101 3.5 29.8 1.0 CG B:ASP105 3.5 32.2 1.0 CA B:ASP105 3.6 23.0 1.0 CG B:GLU101 3.7 29.5 1.0 N B:ASP105 3.7 25.5 1.0 CA B:GLU101 3.9 24.8 1.0 OE1 B:GLU101 4.1 24.3 1.0 CB B:ASP105 4.1 24.5 1.0 H B:VAL104 4.1 30.7 1.0 O B:HOH467 4.2 44.6 1.0 N B:VAL104 4.2 25.6 1.0 CA B:VAL104 4.2 26.1 1.0 CB B:GLU101 4.3 27.4 1.0 HA B:GLN102 4.3 26.5 1.0 N B:GLN102 4.4 24.1 1.0 HA B:VAL104 4.5 31.3 1.0 H B:ASP105 4.5 30.6 1.0 HB3 B:ASP105 4.5 29.4 1.0 C B:GLN102 4.5 27.9 1.0 HG2 B:GLU101 4.5 35.4 1.0 OD2 B:ASP105 4.6 27.5 1.0 H B:PHE106 4.6 27.8 1.0 N B:ALA103 4.7 26.2 1.0 CA B:GLN102 4.7 22.1 1.0 H B:ALA103 4.7 31.4 1.0 O A:HOH452 4.7 39.4 1.0 C B:ALA103 4.7 29.1 1.0 O B:HOH494 4.8 27.1 1.0 HG23 A:THR235 4.8 52.8 1.0 O B:GLN102 4.8 30.1 1.0 C B:ASP105 4.9 24.8 1.0 HB2 B:ASP105 4.9 29.4 1.0 HB2 B:GLU101 5.0 32.8 1.0 HB3 B:GLU101 5.0 32.8 1.0

Y.Li, P.Dharkar, T.H.Han, M.Serpe, C.H.Lee, M.L.Mayer. Novel Functional Properties of Drosophila Cns Glutamate Receptors. Neuron V. 92 1036 2016.
ISSN: ISSN 1097-4199
PubMed: 27889096
DOI: 10.1016/J.NEURON.2016.10.058