Zinc in PDB 1m5e: X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution

The structure of X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution, PDB code: 1m5e was solved by A.Hogner, J.S.Kastrup, R.Jin, T.Liljefors, M.L.Mayer, J.Egebjerg, I.K.Larsen, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.75 / 1.46
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.045, 163.156, 46.773, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 21.6

The binding sites of Zinc atom in the X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution (pdb code 1m5e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution, PDB code: 1m5e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1704 b:23.6 occ:1.00 O A:HOH2016 1.9 37.4 1.0 NE2 A:HIS23 2.1 21.3 1.0 O A:HOH2015 2.2 37.8 1.0 CE1 A:HIS23 3.1 21.0 1.0 CD2 A:HIS23 3.1 21.8 1.0 O A:HOH2014 3.7 42.5 1.0 ND1 A:HIS23 4.2 21.7 1.0 CG A:HIS23 4.2 22.2 1.0 CB A:MET19 4.8 18.1 1.0 O A:HOH1996 5.0 35.3 1.0 CG A:MET19 5.0 21.5 1.0

Zinc binding site 2 out of 8 in the X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1705 b:15.9 occ:1.00 O A:HOH2011 2.0 14.8 1.0 OE1 A:GLU42 2.0 14.0 1.0 OE1 B:GLU166 2.0 18.4 1.0 NE2 A:HIS46 2.1 16.2 1.0 OE2 B:GLU166 2.6 19.6 1.0 CD B:GLU166 2.7 15.6 1.0 CD A:GLU42 2.9 15.2 1.0 CD2 A:HIS46 3.0 14.9 1.0 CE1 A:HIS46 3.1 17.8 1.0 OE2 A:GLU42 3.3 15.7 1.0 ZN B:ZN1711 3.4 23.6 1.0 O B:HOH2094 4.0 35.9 1.0 CD2 A:LEU241 4.1 19.6 1.0 O B:HOH1944 4.1 30.8 1.0 CG B:GLU166 4.1 16.6 1.0 ND1 A:HIS46 4.2 17.2 1.0 CG A:HIS46 4.2 15.1 1.0 N B:SER168 4.2 14.1 1.0 CG A:GLU42 4.3 13.7 1.0 CB B:SER168 4.6 13.9 1.0 CB A:GLU42 4.7 12.4 1.0 CA B:SER168 4.7 13.1 1.0 O B:ALA165 4.7 14.5 1.0 CB B:GLU166 4.8 15.3 1.0 O B:HOH2095 4.8 25.2 1.0 C B:PRO167 4.9 15.4 1.0 CA B:GLU166 5.0 15.9 1.0 CA B:PRO167 5.0 16.2 1.0

Zinc binding site 3 out of 8 in the X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1710 b:27.2 occ:1.00 O B:HOH2095 2.0 25.2 1.0 O B:HOH2057 2.1 21.7 1.0 O B:ACT1703 2.1 31.3 1.0 O B:HOH2098 2.3 39.0 1.0 C B:ACT1703 2.8 31.5 1.0 OXT B:ACT1703 2.8 30.5 1.0 ZN B:ZN1711 3.3 23.6 1.0 CE A:LYS45 3.5 34.1 1.0 O B:HOH1944 3.7 30.8 1.0 CD2 B:PHE170 3.7 15.2 1.0 OG B:SER168 3.9 13.5 1.0 O B:HOH1792 4.1 26.0 1.0 NZ B:LYS144 4.1 20.3 1.0 CG A:LYS45 4.3 27.9 1.0 CH3 B:ACT1703 4.3 30.2 1.0 CE2 B:PHE170 4.3 15.3 1.0 NZ A:LYS45 4.5 36.3 1.0 OD1 B:ASP139 4.5 27.6 1.0 CD A:LYS45 4.5 31.6 1.0 OD2 B:ASP139 4.6 30.1 1.0 O B:HOH2094 4.6 35.9 1.0 O A:HOH2011 4.6 14.8 1.0 CG B:PHE170 4.7 13.2 1.0 CB B:PHE170 4.9 13.5 1.0 CB B:SER168 4.9 13.9 1.0 CG B:ASP139 5.0 24.1 1.0

Zinc binding site 4 out of 8 in the X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1706 b:18.4 occ:1.00 NE2 B:HIS23 2.0 16.1 1.0 OE2 B:GLU30 2.0 16.1 1.0 CD B:GLU30 2.8 14.2 1.0 OE1 B:GLU30 2.9 17.5 1.0 CE1 B:HIS23 3.0 14.9 1.0 CD2 B:HIS23 3.0 16.4 1.0 CD B:LYS20 4.0 17.1 1.0 NZ B:LYS20 4.0 19.3 1.0 ND1 B:HIS23 4.1 15.6 1.0 CG B:HIS23 4.1 15.2 1.0 CG B:GLU30 4.2 17.5 1.0 O B:GLU30 4.3 15.5 1.0 CD1 B:LEU26 4.7 23.9 1.0 CE B:LYS20 4.7 18.6 1.0

Zinc binding site 5 out of 8 in the X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1707 b:16.4 occ:1.00 O B:HOH1819 2.0 21.9 1.0 OE1 B:GLU42 2.0 14.4 1.0 NE2 B:HIS46 2.0 15.8 1.0 CD B:GLU42 2.9 15.4 1.0 CD2 B:HIS46 3.0 13.5 1.0 CE1 B:HIS46 3.0 15.8 1.0 OE2 B:GLU42 3.2 18.6 1.0 CD2 B:LEU241 3.6 14.3 1.0 OE1 B:GLN244 3.8 23.1 1.0 NZ B:LYS45 3.8 18.0 1.0 CE B:LYS45 3.9 18.9 1.0 ND1 B:HIS46 4.1 15.2 1.0 CG B:HIS46 4.1 15.0 1.0 CG B:GLU42 4.2 13.8 1.0 NE2 B:GLN244 4.4 23.1 1.0 CD B:GLN244 4.5 21.3 1.0 CB B:GLU42 4.7 12.8 1.0 O B:HOH1864 4.8 32.2 1.0

Zinc binding site 6 out of 8 in the X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1709 b:30.0 occ:1.00 O B:HOH1959 2.0 28.7 1.0 O B:HOH2096 2.1 41.8 1.0 ND1 B:HIS46 2.1 15.2 1.0 O B:HOH1929 2.2 28.7 1.0 O B:HOH1849 3.0 22.5 1.0 CE1 B:HIS46 3.0 15.8 1.0 CG B:HIS46 3.2 15.0 1.0 CD B:LYS240 3.5 23.4 1.0 CB B:HIS46 3.6 13.9 1.0 NZ B:LYS240 3.6 30.0 1.0 O B:HOH2071 3.8 38.1 1.0 CA B:HIS46 4.0 15.2 1.0 CE B:LYS240 4.1 25.4 1.0 NE2 B:HIS46 4.2 15.8 1.0 O B:HIS46 4.2 18.7 1.0 CD2 B:HIS46 4.3 13.5 1.0 O B:HOH1877 4.4 25.1 1.0 C B:HIS46 4.6 15.7 1.0 CG B:LYS240 4.7 18.3 1.0

Zinc binding site 7 out of 8 in the X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1711 b:23.6 occ:1.00 O A:HOH2011 1.7 14.8 1.0 O B:HOH2095 1.8 25.2 1.0 O B:HOH2094 2.0 35.9 1.0 O B:HOH1944 2.1 30.8 1.0 ZN A:ZN1710 3.3 27.2 1.0 ZN A:ZN1705 3.4 15.9 1.0 OXT B:ACT1703 3.5 30.5 1.0 OG B:SER168 3.8 13.5 1.0 CB B:SER168 3.9 13.9 1.0 O B:HOH2098 3.9 39.0 1.0 NE2 A:HIS46 4.1 16.2 1.0 OE2 B:GLU166 4.1 19.6 1.0 CE1 A:HIS46 4.3 17.8 1.0 CA B:SER168 4.3 13.1 1.0 O B:HOH1741 4.4 15.9 1.0 C B:ACT1703 4.4 31.5 1.0 O B:ACT1703 4.6 31.3 1.0 OE1 B:GLU166 4.7 18.4 1.0 CG A:LYS45 4.7 27.9 1.0 O B:ALA165 4.8 14.5 1.0 CD B:GLU166 4.8 15.6 1.0 OE1 A:GLU42 4.9 14.0 1.0 N B:SER168 4.9 14.1 1.0 CD2 A:HIS46 4.9 14.9 1.0 O B:HOH2057 4.9 21.7 1.0

Zinc binding site 8 out of 8 in the X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Structure of the GLUR2 Ligand Binding Core (S1S2J) in Complex with Acpa at 1.46 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1708 b:37.5 occ:1.00 OE1 C:GLU42 2.1 26.6 1.0 NE2 C:HIS46 2.3 33.0 1.0 CD C:GLU42 3.2 26.4 1.0 CE1 C:HIS46 3.2 32.9 1.0 CD2 C:HIS46 3.3 31.8 1.0 OE2 C:GLU42 3.6 29.9 1.0 CD2 C:LEU241 3.9 20.6 1.0 ND1 C:HIS46 4.3 32.1 1.0 CG C:HIS46 4.4 30.6 1.0 CG C:GLU42 4.4 23.0 1.0 NE2 C:GLN244 4.5 34.9 1.0 CD C:LYS45 4.6 32.6 1.0 CB C:GLU42 4.8 20.2 1.0 NZ C:LYS45 4.9 37.8 1.0

A.Hogner, J.S.Kastrup, R.Jin, T.Liljefors, M.L.Mayer, J.Egebjerg, I.K.Larsen, E.Gouaux. Structural Basis For Ampa Receptor Activation and Ligand Selectivity: Crystal Structures of Five Agonist Complexes with the GLUR2 Ligand-Binding Core J.Mol.Biol. V. 322 93 2002.
ISSN: ISSN 0022-2836
PubMed: 12215417
DOI: 10.1016/S0022-2836(02)00650-2