Zinc in PDB 4lz8: Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators

The structure of Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators, PDB code: 4lz8 was solved by J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.66 / 1.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.676, 164.953, 47.498, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.2

The structure of Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Zinc atom in the Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators (pdb code 4lz8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators, PDB code: 4lz8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:39.9 occ:1.00 OE1 B:GLU678 1.7 19.8 1.0 OE1 A:GLU431 2.1 18.7 1.0 NE2 A:HIS435 2.3 30.2 1.0 CD B:GLU678 2.5 24.6 1.0 OE2 B:GLU678 2.6 25.9 1.0 CD A:GLU431 2.9 18.0 1.0 OE2 A:GLU431 3.2 16.6 1.0 CD2 A:HIS435 3.2 30.2 1.0 CE1 A:HIS435 3.3 32.2 1.0 CG B:GLU678 4.0 24.2 1.0 CD2 A:LEU753 4.1 20.9 1.0 CG A:GLU431 4.3 10.8 1.0 N B:SER680 4.3 15.2 1.0 ND1 A:HIS435 4.4 30.9 1.0 CG A:HIS435 4.4 28.9 1.0 O B:ALA677 4.5 17.9 1.0 CB A:GLU431 4.6 10.2 1.0 CB B:GLU678 4.6 22.6 1.0 CB B:SER680 4.8 13.9 1.0 CA B:SER680 4.9 13.7 1.0 CA B:GLU678 4.9 20.8 1.0 CA B:PRO679 4.9 19.9 1.0 C B:PRO679 4.9 18.0 1.0

Zinc binding site 2 out of 5 in the Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:43.5 occ:1.00 O B:HOH1003 1.8 35.2 1.0 NE2 B:HIS412 2.0 30.9 1.0 OE2 B:GLU419 2.2 26.1 1.0 CD B:GLU419 2.9 26.4 1.0 CD2 B:HIS412 2.9 31.2 1.0 OE1 B:GLU419 2.9 28.7 1.0 CE1 B:HIS412 3.0 32.5 1.0 ND1 B:HIS412 4.1 31.0 1.0 CG B:HIS412 4.1 29.9 1.0 CD B:LYS409 4.1 25.9 1.0 NZ B:LYS409 4.1 32.7 1.0 CG B:GLU419 4.4 27.7 1.0 O B:GLU419 4.4 24.6 1.0 CD2 B:LEU415 4.5 51.1 1.0 CE B:LYS409 4.8 27.6 1.0

Zinc binding site 3 out of 5 in the Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn803 b:48.0 occ:1.00 NE2 B:HIS435 2.1 31.5 1.0 OE1 B:GLU431 2.2 27.3 1.0 CD2 B:HIS435 3.0 30.3 1.0 CE1 B:HIS435 3.1 37.5 1.0 CD B:GLU431 3.1 21.7 1.0 OE2 B:GLU431 3.4 27.1 1.0 CD2 B:LEU753 3.5 18.3 1.0 OE1 B:GLN756 3.5 46.7 1.0 NZ B:LYS434 3.9 35.0 1.0 CE B:LYS434 4.0 32.3 1.0 CG B:HIS435 4.2 30.4 1.0 ND1 B:HIS435 4.2 36.6 1.0 CD B:GLN756 4.4 37.1 1.0 CG B:GLU431 4.5 16.9 1.0 NE2 B:GLN756 4.6 42.5 1.0 CB B:GLU431 4.8 12.6 1.0 CG B:LEU753 4.9 14.3 1.0

Zinc binding site 4 out of 5 in the Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:37.5 occ:1.00 O C:HOH986 1.9 33.3 1.0 O C:HOH949 2.2 39.4 1.0 OD2 C:ASP454 2.2 16.9 1.0 OD1 C:ASP454 2.7 18.7 1.0 CG C:ASP454 2.7 17.3 1.0 OD2 C:ASP456 3.3 42.2 1.0 CB C:ASP454 4.2 16.6 1.0 CG C:ASP456 4.3 40.5 1.0 CB C:ASP456 4.4 37.4 1.0 CG2 C:THR457 4.8 30.7 1.0 N C:ASP456 5.0 29.9 1.0 CA C:ASP454 5.0 17.7 1.0

Zinc binding site 5 out of 5 in the Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structures of GLUR2 Ligand-Binding-Domain in Complex with Glutamate and Positive Allosteric Modulators within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn802 b:0.0 occ:1.00 OE1 C:GLU431 2.4 41.8 1.0 NE2 C:HIS435 3.4 73.5 1.0 CD C:GLU431 3.5 36.5 1.0 CD2 C:HIS435 3.5 69.0 1.0 CE C:LYS434 3.9 56.9 1.0 OE2 C:GLU431 4.0 41.0 1.0 NZ C:LYS434 4.0 59.4 1.0 CD2 C:LEU753 4.3 29.3 1.0 OE1 C:GLN756 4.5 49.1 1.0 CE1 C:HIS435 4.7 73.4 1.0 CG C:GLU431 4.7 28.5 1.0 CG C:HIS435 4.9 63.3 1.0 CB C:GLU431 4.9 25.6 1.0

N.C.Patel, J.Schwarz, X.J.Hou, D.J.Hoover, L.Xie, A.J.Fliri, R.J.Gallaschun, J.T.Lazzaro, D.K.Bryce, W.E.Hoffmann, A.N.Hanks, D.Mcginnis, E.S.Marr, J.L.Gazard, M.Hajos, R.J.Scialis, R.S.Hurst, C.L.Shaffer, J.Pandit, C.J.O'donnell. Discovery and Characterization of A Novel Dihydroisoxazole Class of Alpha-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid (Ampa) Receptor Potentiators. J.Med.Chem. V. 56 9180 2013.
ISSN: ISSN 0022-2623
PubMed: 24215237
DOI: 10.1021/JM401274B