Zinc in PDB 3il1: Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21

The structure of Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21, PDB code: 3il1 was solved by A.H.Ahmed, C.P.Ptak, R.E.Oswald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.02 / 2.00
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.327, 114.711, 165.366, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.4

The structure of Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21 (pdb code 3il1). 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 Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21, PDB code: 3il1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn263 b:41.5 occ:1.00 OE2 B:GLU42 1.8 35.0 1.0 OE1 H:GLU166 2.0 22.3 1.0 NE2 B:HIS46 2.1 25.9 1.0 CD H:GLU166 2.7 30.4 1.0 CD B:GLU42 2.8 26.3 1.0 OE2 H:GLU166 2.8 27.6 1.0 CD2 B:HIS46 2.9 26.6 1.0 OE1 B:GLU42 3.1 1.4 1.0 O H:HOH265 3.2 15.3 1.0 CE1 B:HIS46 3.3 27.5 1.0 CD B:LYS45 3.8 37.9 1.0 CD2 B:LEU241 4.1 19.9 1.0 CG B:HIS46 4.1 27.0 1.0 CG B:GLU42 4.1 30.9 1.0 CG H:GLU166 4.2 23.2 1.0 ND1 B:HIS46 4.3 25.7 1.0 N H:SER168 4.3 21.7 1.0 CB B:GLU42 4.5 25.1 1.0 O H:ALA165 4.6 21.9 1.0 CB H:SER168 4.7 19.9 1.0 CB H:GLU166 4.8 25.1 1.0 CA H:SER168 4.8 20.8 1.0 CG B:LYS45 4.8 34.7 1.0 CE B:LYS45 4.9 44.1 1.0 CA B:GLU42 4.9 22.8 1.0 O B:GLU42 5.0 25.8 1.0 C H:PRO167 5.0 22.5 1.0 CA H:GLU166 5.0 20.4 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1 b:30.0 occ:1.00 OE1 E:GLU42 1.9 23.6 1.0 NE2 E:HIS46 2.6 38.3 1.0 CD E:GLU42 2.8 41.4 1.0 OE2 E:GLU42 3.3 51.1 1.0 CD2 E:HIS46 3.4 33.4 1.0 CE1 E:HIS46 3.7 42.4 1.0 CD2 E:LEU241 3.9 30.4 1.0 O E:HOH275 3.9 38.0 1.0 CG E:GLU42 4.1 40.3 1.0 CD E:LYS45 4.3 44.0 1.0 CG E:HIS46 4.6 39.3 1.0 ND1 E:HIS46 4.7 38.3 1.0 CB E:GLU42 4.7 35.4 1.0 CD2 E:LEU246 4.9 34.3 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn262 b:9.9 occ:1.00 OD2 E:ASP65 2.2 32.4 1.0 OD1 E:ASP65 2.7 31.7 1.0 CG E:ASP65 2.8 29.4 1.0 O E:HOH743 3.0 42.5 1.0 CB E:ASP65 4.3 31.2 1.0 O E:HOH470 4.4 39.9 1.0 CG2 E:THR68 4.5 35.9 1.0 CB E:ASP67 4.6 41.9 1.0 N E:ASP67 5.0 37.0 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn2 b:29.8 occ:1.00 NE2 H:HIS23 2.0 23.4 1.0 OE2 H:GLU30 2.1 60.3 1.0 CE1 H:HIS23 2.8 28.9 1.0 CD H:GLU30 2.9 50.3 1.0 OE1 H:GLU30 3.0 44.6 1.0 CD2 H:HIS23 3.2 28.2 1.0 ND1 H:HIS23 4.0 23.0 1.0 CD H:LYS20 4.1 25.1 1.0 NZ H:LYS20 4.1 29.1 1.0 CG H:HIS23 4.2 24.5 1.0 CG H:GLU30 4.3 45.0 1.0 O H:GLU30 4.7 28.4 1.0 CE H:LYS20 4.7 25.3 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Ampa Subunit GLUR2 Bound to the Allosteric Modulator, Idra-21 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn3 b:26.8 occ:1.00 OE1 H:GLU42 2.0 1.4 1.0 NE2 H:HIS46 2.1 25.4 1.0 CD H:GLU42 2.9 25.6 1.0 CD2 H:HIS46 3.0 25.5 1.0 CE1 H:HIS46 3.2 26.9 1.0 OE2 H:GLU42 3.2 43.9 1.0 CD2 H:LEU241 3.4 19.4 1.0 O H:HOH371 3.6 47.3 1.0 OE1 H:GLN244 3.6 34.9 1.0 CE H:LYS45 3.9 41.4 1.0 NZ H:LYS45 3.9 47.8 1.0 CG H:HIS46 4.2 26.0 1.0 CG H:GLU42 4.2 31.2 1.0 ND1 H:HIS46 4.2 28.9 1.0 CB H:GLU42 4.5 30.4 1.0 CD2 H:LEU246 4.6 32.8 1.0 CD H:GLN244 4.6 36.3 1.0 NE2 H:GLN244 4.9 34.8 1.0 CG H:LEU241 4.9 17.7 1.0

C.P.Ptak, A.H.Ahmed, R.E.Oswald. Probing the Allosteric Modulator Binding Site of GLUR2 with Thiazide Derivatives Biochemistry V. 48 8594 2009.
ISSN: ISSN 0006-2960
PubMed: 19673491
DOI: 10.1021/BI901127S