Zinc in PDB 3lsl: Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form)

The structure of Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form), PDB code: 3lsl was solved by A.H.Ahmed, R.E.Oswald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.88 / 2.12
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.528, 114.343, 163.829, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 26.3

The binding sites of Zinc atom in the Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form) (pdb code 3lsl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form), PDB code: 3lsl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:31.8 occ:1.00 NE2 A:HIS23 1.6 49.0 1.0 CE1 A:HIS23 2.0 35.1 1.0 O A:HOH434 2.6 28.3 1.0 CD2 A:HIS23 2.9 38.0 1.0 ND1 A:HIS23 3.3 37.7 1.0 CG A:HIS23 3.7 35.1 1.0 OE1 A:GLU24 4.2 20.0 1.0 CG A:GLU24 4.5 20.0 1.0 CD A:GLU24 4.7 20.0 1.0

Zinc binding site 2 out of 5 in the Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:44.8 occ:1.00 NE2 A:HIS46 2.5 53.6 1.0 NZ A:LYS45 3.1 52.6 1.0 CE1 A:HIS46 3.1 55.4 1.0 OE1 A:GLU42 3.6 41.3 1.0 CE A:LYS45 3.7 45.1 1.0 CD2 A:HIS46 3.7 43.6 1.0 OE2 A:GLU42 4.2 45.0 1.0 CD A:GLU42 4.2 42.2 1.0 CD2 A:LEU241 4.2 41.5 1.0 OE1 A:GLN244 4.3 65.3 1.0 ND1 A:HIS46 4.4 51.6 1.0 CG A:HIS46 4.7 42.2 1.0

Zinc binding site 3 out of 5 in the Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn3 b:46.4 occ:1.00 NE2 D:HIS23 2.2 49.0 1.0 CD2 D:HIS23 2.8 38.1 1.0 CE1 D:HIS23 3.2 46.9 1.0 O D:HOH408 3.7 54.4 1.0 CG D:HIS23 3.9 40.5 1.0 ND1 D:HIS23 4.0 49.4 1.0 CG D:MET19 4.2 41.9 1.0 CB D:MET19 4.7 34.7 1.0

Zinc binding site 4 out of 5 in the Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn400 b:47.5 occ:1.00 OE1 G:GLU166 2.0 40.0 1.0 NE2 D:HIS46 2.1 33.2 1.0 OE1 D:GLU42 2.2 34.5 1.0 CD G:GLU166 2.8 32.2 1.0 CG G:GLU166 2.8 32.0 1.0 CE1 D:HIS46 3.0 35.8 1.0 CD2 D:HIS46 3.1 31.1 1.0 CD D:GLU42 3.1 33.8 1.0 OE2 D:GLU42 3.3 24.8 1.0 CB G:GLU166 3.9 36.0 1.0 OE2 G:GLU166 4.0 1.2 1.0 ND1 D:HIS46 4.1 26.9 1.0 N G:SER168 4.2 24.2 1.0 CG D:HIS46 4.2 27.3 1.0 CB G:SER168 4.3 23.8 1.0 CD2 D:LEU241 4.3 35.1 1.0 CG D:GLU42 4.5 24.4 1.0 CA G:SER168 4.6 26.6 1.0 O G:ALA165 4.7 25.3 1.0 C G:PRO167 5.0 30.4 1.0 CB D:GLU42 5.0 24.8 1.0 CA G:GLU166 5.0 26.1 1.0

Zinc binding site 5 out of 5 in the Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Piracetam Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn401 b:50.9 occ:1.00 NE2 G:HIS46 2.2 23.2 1.0 OE2 G:GLU42 2.3 20.0 1.0 CE1 G:HIS46 2.7 35.0 1.0 CD G:GLU42 3.2 20.0 1.0 CD2 G:HIS46 3.5 27.6 1.0 CG G:GLU42 3.5 20.0 1.0 OE1 G:GLN244 3.9 41.9 1.0 ND1 G:HIS46 4.0 30.9 1.0 NZ G:LYS45 4.0 29.5 1.0 CD2 G:LEU241 4.1 28.8 1.0 CE G:LYS45 4.2 30.9 1.0 OE1 G:GLU42 4.4 20.0 1.0 CG G:HIS46 4.4 29.4 1.0

A.H.Ahmed, R.E.Oswald. Piracetam Defines A New Binding Site For Allosteric Modulators of Alpha-Amino-3-Hydroxy-5-Methyl-4-Isoxazole-Propionic Acid (Ampa) Receptors. J.Med.Chem. V. 53 2197 2010.
ISSN: ISSN 0022-2623
PubMed: 20163115
DOI: 10.1021/JM901905J