Zinc in PDB 3bft: Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution

The structure of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution, PDB code: 3bft was solved by M.Beich-Frandsen, O.Mirza, 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)	20.00 / 2.27
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.820, 163.333, 47.270, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25

The structure of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution also contains other interesting chemical elements:

Arsenic	(As)	1 atom
Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution (pdb code 3bft). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution, PDB code: 3bft:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:61.5 occ:1.00 NE2 A:HIS46 2.2 56.1 1.0 OE1 A:GLU42 2.4 41.0 1.0 CE1 A:HIS46 3.0 56.1 1.0 CD2 A:HIS46 3.3 55.2 1.0 NZ A:LYS45 3.4 48.4 1.0 CD A:GLU42 3.5 42.0 1.0 CE A:LYS45 3.6 48.7 1.0 OE2 A:GLU42 3.8 47.0 1.0 CD2 A:LEU241 4.2 32.6 1.0 ND1 A:HIS46 4.2 55.0 1.0 CG A:HIS46 4.4 53.4 1.0 OE1 A:GLN244 4.7 51.6 1.0 CG A:GLU42 4.8 39.9 1.0

Zinc binding site 2 out of 5 in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:40.5 occ:1.00 OD2 A:ASP65 2.1 34.1 1.0 CG A:ASP65 2.9 34.1 1.0 OD1 A:ASP65 3.0 38.7 1.0 OD2 A:ASP67 3.8 52.8 1.0 CB A:ASP65 4.3 33.9 1.0 CB A:ASP67 4.6 45.0 1.0 CG A:ASP67 4.7 48.9 1.0

Zinc binding site 3 out of 5 in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:32.7 occ:1.00 OE2 B:GLU30 2.0 40.0 1.0 NE2 B:HIS23 2.1 26.6 1.0 CD B:GLU30 2.8 39.7 1.0 CD2 B:HIS23 3.0 27.0 1.0 OE1 B:GLU30 3.0 40.3 1.0 CE1 B:HIS23 3.2 25.7 1.0 NZ B:LYS20 4.1 26.7 1.0 CD B:LYS20 4.2 30.4 1.0 CG B:HIS23 4.2 27.7 1.0 ND1 B:HIS23 4.2 27.2 1.0 CG B:GLU30 4.3 36.4 1.0 O B:GLU30 4.4 28.4 1.0 CD1 B:LEU26 4.6 47.5 1.0 CE B:LYS20 4.8 27.6 1.0

Zinc binding site 4 out of 5 in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:32.0 occ:1.00 NE2 B:HIS46 2.0 26.7 1.0 OE1 B:GLU42 2.3 32.9 1.0 CE1 B:HIS46 2.7 31.1 1.0 CD B:GLU42 3.1 30.7 1.0 CD2 B:HIS46 3.2 29.5 1.0 OE2 B:GLU42 3.3 32.0 1.0 CD2 B:LEU241 3.5 23.1 1.0 OE1 B:GLN244 3.8 41.3 1.0 NZ B:LYS45 3.9 29.9 1.0 ND1 B:HIS46 3.9 30.4 1.0 CE B:LYS45 4.1 29.5 1.0 CG B:HIS46 4.2 30.6 1.0 CG B:GLU42 4.4 29.5 1.0 CB B:GLU42 4.8 24.3 1.0 CD2 B:LEU246 4.9 29.6 1.0 CD B:GLN244 4.9 39.5 1.0

Zinc binding site 5 out of 5 in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1005 b:25.6 occ:1.00 OE1 B:GLU166 1.9 27.2 1.0 O1 B:CAC1439 2.1 47.2 1.0 OE2 B:GLU166 2.4 26.4 1.0 CD B:GLU166 2.5 27.5 1.0 AS B:CAC1439 3.2 50.2 1.0 O2 B:CAC1439 3.5 46.9 1.0 C1 B:CAC1439 3.9 48.6 1.0 CG B:GLU166 4.0 24.8 1.0 N B:SER168 4.3 24.6 1.0 CB B:GLU166 4.6 26.6 1.0 O B:ALA165 4.7 24.4 1.0 CB B:SER168 4.7 22.5 1.0 CA B:SER168 4.8 23.4 1.0 CA B:GLU166 4.9 25.8 1.0 C2 B:CAC1439 5.0 49.3 1.0

M.Beich-Frandsen, D.S.Pickering, O.Mirza, T.N.Johansen, J.Greenwood, B.Vestergaard, A.Schousboe, M.Gajhede, T.Liljefors, J.S.Kastrup. Structures of the Ligand-Binding Core of IGLUR2 in Complex with the Agonists (R)- and (S)-2-Amino-3-(4-Hydroxy-1,2,5-Thiadiazol-3-Yl)Propionic Acid Explain Their Unusual Equipotency. J.Med.Chem. V. 51 1459 2008.
ISSN: ISSN 0022-2623
PubMed: 18269227
DOI: 10.1021/JM701126W