Sodium in PDB 2v3u: Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in Complex with D-Serine

The structure of Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in Complex with D-Serine, PDB code: 2v3u was solved by P.Naur, B.Vestergaard, M.Gajhede, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.19 / 1.74
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.801, 40.307, 44.393, 66.88, 79.31, 86.46
R / Rfree (%)	19.7 / 25

The structure of Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in Complex with D-Serine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in Complex with D-Serine (pdb code 2v3u). 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 Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in Complex with D-Serine, PDB code: 2v3u:

Sodium binding site 1 out of 1 in the Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in Complex with D-Serine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in Complex with D-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1263 b:26.2 occ:1.00 OD1 A:ASP97 2.3 23.9 1.0 O A:GLU93 2.3 22.2 1.0 O A:HOH2054 2.3 29.7 1.0 OE2 A:GLU93 2.4 24.7 1.0 O A:HOH2114 2.5 30.2 1.0 O A:VAL96 2.6 19.8 1.0 CD A:GLU93 3.3 24.9 1.0 C A:VAL96 3.4 19.3 1.0 C A:GLU93 3.5 21.8 1.0 CG A:ASP97 3.5 23.5 1.0 CA A:ASP97 3.8 19.5 1.0 CG A:GLU93 3.8 23.1 1.0 ND1 A:HIS228 3.8 27.2 1.0 N A:ASP97 3.9 19.4 1.0 CA A:GLU93 4.1 20.4 1.0 OE1 A:GLU93 4.2 23.1 1.0 CB A:ASP97 4.2 19.6 1.0 N A:VAL96 4.4 20.6 1.0 CE1 A:HIS228 4.4 26.4 1.0 CA A:VAL96 4.5 19.9 1.0 OD2 A:ASP97 4.5 21.9 1.0 N A:ASN94 4.5 23.6 1.0 CB A:GLU93 4.6 19.5 1.0 C A:ASN94 4.6 24.6 1.0 O A:HOH2118 4.6 27.2 1.0 CG A:HIS228 4.7 26.0 1.0 CA A:ASN94 4.8 24.8 1.0 N A:VAL95 4.8 23.5 1.0 O A:ASN94 4.8 25.9 1.0

P.Naur, K.B.Hansen, A.S.Kristensen, S.M.Dravid, D.S.Pickering, L.Olsen, B.Vestergaard, J.Egebjerg, M.Gajhede, S.F.Traynelis, J.S.Kastrup. Ionotropic Glutamate-Like Receptor {Delta}2 Binds D-Serine and Glycine. Proc.Natl.Acad.Sci.Usa V. 104 14116 2007.
ISSN: ISSN 0027-8424
PubMed: 17715062
DOI: 10.1073/PNAS.0703718104