Zinc in PDB 3rn8: Crystal Structure of IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator

The structure of Crystal Structure of IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator, PDB code: 3rn8 was solved by D.E.Timm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.96 / 1.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.889, 163.232, 47.356, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.4

The binding sites of Zinc atom in the Crystal Structure of IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator (pdb code 3rn8). 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 IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator, PDB code: 3rn8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator


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 IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn282 b:18.9 occ:1.00 OE2 B:GLU166 1.7 16.5 1.0 OE1 A:GLU42 2.0 16.0 1.0 NE2 A:HIS46 2.1 16.7 1.0 O1 B:SO4286 2.1 23.9 1.0 CD B:GLU166 2.6 18.0 1.0 OE1 B:GLU166 2.8 21.0 1.0 CD A:GLU42 2.9 16.5 1.0 CD2 A:HIS46 3.0 19.0 1.0 CE1 A:HIS46 3.1 20.1 1.0 OE2 A:GLU42 3.2 16.5 1.0 S B:SO4286 3.3 23.8 1.0 O2 B:SO4286 3.7 28.8 1.0 O3 B:SO4286 3.8 35.6 1.0 CG B:GLU166 4.1 19.4 1.0 CD2 A:LEU241 4.1 15.8 1.0 CG A:HIS46 4.2 17.3 1.0 ND1 A:HIS46 4.2 19.7 1.0 CG A:GLU42 4.2 13.6 1.0 N B:SER168 4.3 14.6 1.0 O4 B:SO4286 4.5 30.8 1.0 CB A:GLU42 4.7 13.6 1.0 O B:ALA165 4.7 16.3 1.0 CB B:GLU166 4.7 16.3 1.0 CB B:SER168 4.8 15.7 1.0 CA B:SER168 4.8 14.8 1.0 CE A:LYS45 4.8 32.2 1.0 CA B:GLU166 5.0 17.1 1.0 C B:PRO167 5.0 15.5 1.0 CA B:PRO167 5.0 15.3 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator


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 IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn283 b:21.9 occ:1.00 NE2 B:HIS23 2.0 19.3 1.0 OE1 B:GLU30 2.0 22.7 1.0 O B:HOH732 2.2 29.1 1.0 CD B:GLU30 2.8 20.3 1.0 OE2 B:GLU30 2.9 22.0 1.0 CD2 B:HIS23 2.9 17.3 1.0 CE1 B:HIS23 3.0 15.3 1.0 CD B:LYS20 4.1 18.9 1.0 CG B:HIS23 4.1 20.7 1.0 ND1 B:HIS23 4.1 20.4 1.0 NZ B:LYS20 4.1 21.4 1.0 CG B:GLU30 4.3 21.9 1.0 O B:GLU30 4.3 17.7 1.0 CD2 B:LEU26 4.6 38.0 1.0 CE B:LYS20 4.7 19.3 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator


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 IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn284 b:20.8 occ:1.00 NE2 B:HIS46 2.0 18.8 1.0 OE1 B:GLU42 2.1 18.4 1.0 O B:HOH516 2.1 23.8 1.0 CE1 B:HIS46 3.0 20.8 1.0 CD2 B:HIS46 3.0 16.3 1.0 CD B:GLU42 3.0 17.7 1.0 OE2 B:GLU42 3.3 22.3 1.0 OE1 B:GLN244 3.6 30.5 1.0 CD2 B:LEU241 3.6 18.1 1.0 CE B:LYS45 3.9 21.8 1.0 NZ B:LYS45 3.9 21.2 1.0 ND1 B:HIS46 4.1 21.6 1.0 CG B:HIS46 4.1 17.6 1.0 O B:HOH524 4.1 30.6 1.0 CG B:GLU42 4.3 13.7 1.0 CD B:GLN244 4.4 29.9 1.0 NE2 B:GLN244 4.4 28.4 1.0 CB B:GLU42 4.7 13.1 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator


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 IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn281 b:24.6 occ:1.00 O C:HOH815 1.5 23.8 1.0 OD2 C:ASP65 2.1 19.1 1.0 O C:HOH441 2.4 43.1 1.0 CG C:ASP65 2.8 23.6 1.0 OD1 C:ASP65 2.9 26.6 1.0 OD1 C:ASP67 4.0 35.9 1.0 CB C:ASP65 4.3 21.6 1.0 CB C:ASP67 4.6 31.5 1.0 O C:HOH641 4.7 33.2 1.0 CG C:ASP67 4.8 33.9 1.0 O C:HOH597 4.9 33.0 1.0 CG2 C:THR68 5.0 28.1 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator


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 IGLUR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn282 b:93.8 occ:1.00 OE1 C:GLU42 2.5 36.7 1.0 NE2 C:HIS46 2.5 47.8 1.0 CD2 C:HIS46 3.2 47.5 1.0 CD C:GLU42 3.6 35.4 1.0 CD1 C:LEU246 3.6 29.3 0.5 CE1 C:HIS46 3.7 47.8 1.0 CD2 C:LEU241 3.8 24.9 1.0 CD2 C:LEU246 4.0 26.2 0.5 NZ C:LYS45 4.2 45.5 1.0 OE1 C:GLN244 4.2 41.3 1.0 OE2 C:GLU42 4.2 37.7 1.0 CG C:HIS46 4.5 46.0 1.0 CB C:GLU42 4.6 26.5 1.0 CD C:LYS45 4.6 43.3 1.0 CG C:GLU42 4.6 28.4 1.0 ND1 C:HIS46 4.7 48.2 1.0 O C:GLU42 4.7 29.1 1.0 CE C:LYS45 4.8 44.1 1.0 CA C:GLU42 4.9 26.9 1.0 NE2 C:GLN244 5.0 40.2 1.0 CD C:GLN244 5.0 35.2 1.0

D.E.Timm, M.Benveniste, A.M.Weeks, E.S.Nisenbaum, K.M.Partin. Structural and Functional Analysis of Two New Positive Allosteric Modulators of GLUA2 Desensitization and Deactivation. Mol.Pharmacol. V. 80 267 2011.
ISSN: ISSN 0026-895X
PubMed: 21543522
DOI: 10.1124/MOL.110.070243