Sodium in PDB 5cni: MGLU2 with Glutamate

The structure of MGLU2 with Glutamate, PDB code: 5cni was solved by D.K.Clawson, S.Atwell, J.A.Monn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.66 / 2.69
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	156.079, 79.332, 93.603, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 22.2

The structure of MGLU2 with Glutamate also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the MGLU2 with Glutamate (pdb code 5cni). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the MGLU2 with Glutamate, PDB code: 5cni:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the MGLU2 with Glutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of MGLU2 with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:63.3 occ:1.00 O A:HOH754 2.5 52.9 1.0 O A:ILE72 2.6 42.1 1.0 O A:ASP75 2.6 51.8 1.0 O A:LEU78 2.7 43.6 1.0 O A:LEU79 3.1 44.0 1.0 C A:ASP75 3.5 51.5 1.0 N A:ASP75 3.5 45.3 1.0 C A:ILE72 3.7 41.6 1.0 C A:LEU79 3.7 44.0 1.0 C A:ASN73 3.8 45.5 1.0 CA A:ASN73 3.8 38.4 1.0 CA A:PRO80 3.8 40.3 1.0 C A:LEU78 3.9 43.2 1.0 CA A:ASP75 3.9 45.4 1.0 O A:HOH816 4.0 43.7 1.0 O A:ASN73 4.0 47.0 1.0 N A:PRO80 4.0 40.8 1.0 N A:ARG74 4.2 41.5 1.0 N A:ASN73 4.2 38.3 1.0 CB A:ASP75 4.3 46.2 1.0 C A:PRO80 4.4 43.4 1.0 O A:PRO80 4.5 43.4 1.0 C A:ARG74 4.5 47.6 1.0 N A:PRO76 4.7 49.0 1.0 CA A:LEU79 4.7 38.9 1.0 N A:LEU79 4.7 38.2 1.0 O A:VAL82 4.9 44.6 1.0 CA A:ARG74 4.9 41.4 1.0 CA A:LEU78 4.9 41.1 1.0 CB A:LEU79 5.0 39.5 1.0

Sodium binding site 2 out of 2 in the MGLU2 with Glutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of MGLU2 with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:46.4 occ:1.00 O B:ILE72 2.2 33.6 1.0 O B:HOH708 2.2 34.7 1.0 O B:LEU78 2.2 36.5 1.0 O B:HOH714 2.3 36.5 1.0 O B:LEU79 2.6 35.8 1.0 C B:LEU79 3.2 37.0 1.0 C B:ILE72 3.3 33.0 1.0 C B:LEU78 3.4 36.9 1.0 O B:ASP75 3.5 40.5 1.0 CA B:ASN73 3.8 31.2 1.0 N B:PRO80 3.9 36.4 1.0 CA B:LEU79 3.9 30.9 1.0 O B:HOH758 4.0 41.4 1.0 N B:ASN73 4.0 30.8 1.0 CB B:LEU79 4.0 30.1 1.0 CA B:PRO80 4.0 36.4 1.0 C B:ASN73 4.0 36.5 1.0 N B:LEU79 4.0 32.1 1.0 CG2 B:ILE72 4.2 23.3 1.0 O B:ASN73 4.3 37.2 1.0 N B:ASP75 4.4 36.6 1.0 O B:VAL82 4.4 37.9 1.0 N B:ARG74 4.5 32.4 1.0 CA B:ILE72 4.5 25.8 1.0 C B:ASP75 4.5 41.1 1.0 CA B:LEU78 4.6 34.1 1.0 CB B:ASP75 4.7 37.6 1.0 OD1 B:ASN73 4.8 37.8 1.0 C B:PRO80 4.8 41.0 1.0 CA B:ASP75 4.8 36.5 1.0 O B:HOH807 4.9 41.3 1.0 N B:LEU78 4.9 36.4 1.0 CB B:LEU78 5.0 33.2 1.0

J.A.Monn, L.Prieto, L.Taboada, J.Hao, M.R.Reinhard, S.S.Henry, C.D.Beadle, L.Walton, T.Man, H.Rudyk, B.Clark, D.Tupper, S.R.Baker, C.Lamas, C.Montero, A.Marcos, J.Blanco, M.Bures, D.K.Clawson, S.Atwell, F.Lu, J.Wang, M.Russell, B.A.Heinz, X.Wang, J.H.Carter, B.G.Getman, J.T.Catlow, S.Swanson, B.G.Johnson, D.B.Shaw, D.L.Mckinzie. Synthesis and Pharmacological Characterization of C4-(Thiotriazolyl) -Substituted-2-Aminobicyclo[3.1.0]Hexane-2,6-Dicarboxylates. Identification of (1R,2S,4R,5R,6R)-2-Amino-4-(1H-1,2,4-Triazol-3-Ylsulfanyl) Bicyclo[3.1.0]Hexane-2,6-Dicarboxylic Acid (LY2812223), A Highly Potent, Functionally Selective MGLU2 Receptor Agonist. J.Med.Chem. V. 58 7526 2015.
ISSN: ISSN 0022-2623
PubMed: 26313429
DOI: 10.1021/ACS.JMEDCHEM.5B01124