Calcium in PDB 2v3t: Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in the Apo Form

The structure of Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in the Apo Form, PDB code: 2v3t 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)	30.00 / 2.75
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.971, 91.031, 177.393, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 28.7

The binding sites of Calcium atom in the Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in the Apo Form (pdb code 2v3t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in the Apo Form, PDB code: 2v3t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in the Apo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1264 b:41.8 occ:1.00 OD1 B:ASP234 2.1 37.3 1.0 OD1 A:ASP97 2.3 48.3 1.0 O A:GLU93 2.4 34.5 1.0 O A:VAL96 2.4 40.1 1.0 OE2 A:GLU93 2.4 34.1 1.0 CG B:ASP234 2.9 35.9 1.0 OD2 B:ASP234 3.0 33.5 1.0 C A:VAL96 3.2 38.2 1.0 CG A:ASP97 3.4 45.4 1.0 C A:GLU93 3.6 35.2 1.0 CD A:GLU93 3.6 35.5 1.0 CA A:ASP97 3.8 39.0 1.0 N A:ASP97 3.8 38.9 1.0 O A:ASN94 3.9 33.7 1.0 ND1 A:HIS228 4.0 41.8 1.0 CB A:ASP97 4.2 42.0 1.0 N A:VAL96 4.2 36.2 1.0 CA A:VAL96 4.2 37.0 1.0 CG A:GLU93 4.3 34.6 1.0 OD2 A:ASP97 4.3 47.6 1.0 C A:ASN94 4.3 35.4 1.0 CB B:ASP234 4.4 35.8 1.0 CA A:GLU93 4.4 34.3 1.0 OE1 A:GLU93 4.5 36.5 1.0 N A:ASN94 4.5 36.8 1.0 CA A:ASN94 4.6 36.0 1.0 CE1 A:HIS228 4.7 40.6 1.0 NE2 B:GLN238 4.9 29.9 1.0 C A:VAL95 4.9 36.0 1.0

Calcium binding site 2 out of 2 in the Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in the Apo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Ligand-Binding Core of the Ionotropic Glutamate Receptor-Like GLURDELTA2 in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1264 b:34.7 occ:1.00 OE2 B:GLU93 2.2 22.2 1.0 O B:GLU93 2.3 23.7 1.0 OD1 B:ASP97 2.4 43.8 1.0 OD2 A:ASP234 2.5 48.5 1.0 O B:VAL96 2.5 33.6 1.0 OD1 A:ASP234 2.9 50.5 1.0 CG A:ASP234 3.0 48.1 1.0 CD B:GLU93 3.2 25.3 1.0 C B:VAL96 3.3 33.1 1.0 C B:GLU93 3.4 24.9 1.0 CG B:ASP97 3.6 41.4 1.0 CA B:ASP97 3.7 36.3 1.0 N B:ASP97 3.8 34.6 1.0 CG B:GLU93 3.9 24.6 1.0 N B:VAL96 4.1 29.4 1.0 OE1 B:GLU93 4.1 25.1 1.0 CA B:GLU93 4.2 25.3 1.0 CA B:VAL96 4.3 30.8 1.0 CB B:ASP97 4.3 37.6 1.0 C B:ASN94 4.4 27.3 1.0 N B:ASN94 4.4 26.7 1.0 O B:ASN94 4.5 29.1 1.0 CB A:ASP234 4.5 46.0 1.0 CA B:ASN94 4.6 27.2 1.0 ND1 B:HIS228 4.6 45.2 1.0 OD2 B:ASP97 4.6 43.3 1.0 CB B:GLU93 4.7 26.6 1.0 N B:VAL95 4.7 28.0 1.0 NE2 A:GLN238 4.8 38.2 1.0 C B:VAL95 4.8 27.7 1.0 C B:ASP97 5.0 35.9 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