Zinc in PDB 1ms7: X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate

The structure of X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate, PDB code: 1ms7 was solved by C.Kasper, M.-L.Lunn, T.Liljefors, E.Gouaux, J.Egebjerg, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.56 / 1.97
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.723, 162.863, 47.133, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.3

The binding sites of Zinc atom in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate (pdb code 1ms7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate, PDB code: 1ms7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


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 (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3002 b:53.1 occ:1.00 O A:HOH3184 2.2 54.7 1.0 OE1 A:GLU39 2.2 35.5 1.0 O A:HOH3223 2.2 39.3 1.0 NE2 A:HIS43 2.5 36.1 1.0 O A:HOH3333 3.0 51.8 1.0 CD A:GLU39 3.2 33.9 1.0 NZ A:LYS42 3.3 40.3 1.0 CE1 A:HIS43 3.4 35.6 1.0 CD2 A:HIS43 3.5 33.9 1.0 OE2 A:GLU39 3.6 38.9 1.0 CE A:LYS42 3.6 38.7 1.0 CD2 A:LEU238 4.1 22.6 1.0 O A:HOH3314 4.3 47.7 1.0 OE1 A:GLN241 4.4 45.6 1.0 CG A:GLU39 4.4 31.1 1.0 ND1 A:HIS43 4.6 36.1 1.0 CG A:HIS43 4.7 33.9 1.0 CB A:GLU39 4.9 27.6 1.0

Zinc binding site 2 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


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 (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3003 b:35.4 occ:1.00 OD2 A:ASP62 2.1 26.4 1.0 O A:HOH3326 2.3 33.4 1.0 O A:HOH3076 2.5 41.2 1.0 CG A:ASP62 2.8 26.1 1.0 OD1 A:ASP62 2.8 27.8 1.0 OD2 A:ASP64 4.1 41.1 1.0 CB A:ASP62 4.2 25.4 1.0 CB A:ASP64 4.5 36.7 1.0 CG A:ASP64 4.8 38.9 1.0 CG2 A:THR65 4.9 30.7 1.0 O A:HOH3189 5.0 39.2 1.0

Zinc binding site 3 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


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 (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3001 b:28.2 occ:1.00 NE2 B:HIS20 2.1 24.1 1.0 OE2 B:GLU27 2.1 23.2 1.0 O B:HOH3424 2.1 33.7 1.0 NE2 A:HIS20 2.2 26.4 1.0 CD B:GLU27 2.9 22.9 1.0 OE1 B:GLU27 3.0 21.7 1.0 CD2 B:HIS20 3.0 23.9 1.0 CD2 A:HIS20 3.0 25.2 1.0 CE1 B:HIS20 3.1 24.0 1.0 CE1 A:HIS20 3.2 25.5 1.0 CG A:GLU21 3.6 38.9 1.0 CD B:LYS17 4.0 21.4 1.0 NZ B:LYS17 4.0 23.4 1.0 CG B:HIS20 4.2 23.6 1.0 ND1 B:HIS20 4.2 25.4 1.0 CG A:HIS20 4.2 27.1 1.0 ND1 A:HIS20 4.3 23.8 1.0 O B:GLU27 4.3 20.3 1.0 CD A:GLU21 4.3 40.9 1.0 CG B:GLU27 4.3 21.2 1.0 CE B:LYS17 4.7 20.1 1.0 CD1 B:LEU23 4.7 41.6 1.0 SD A:MET16 4.7 32.5 1.0 CB A:GLU21 4.8 35.5 1.0 OE1 A:GLU21 4.8 39.5 1.0 OE2 A:GLU21 4.9 41.5 1.0 O A:HOH3188 4.9 44.6 1.0

Zinc binding site 4 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


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 (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3004 b:24.1 occ:1.00 NE2 B:HIS43 1.9 17.6 1.0 O B:HOH3453 2.1 25.5 1.0 OE1 B:GLU39 2.2 20.9 1.0 CE1 B:HIS43 2.8 21.7 1.0 CD2 B:HIS43 2.9 19.1 1.0 CD B:GLU39 3.0 21.1 1.0 OE2 B:GLU39 3.3 21.7 1.0 CD2 B:LEU238 3.6 17.1 1.0 OE1 B:GLN241 3.6 31.4 1.0 NZ B:LYS42 3.7 19.9 1.0 CE B:LYS42 3.7 21.7 1.0 ND1 B:HIS43 4.0 20.4 1.0 CG B:HIS43 4.0 19.9 1.0 O B:HOH3388 4.2 44.2 1.0 CG B:GLU39 4.4 18.8 1.0 CD B:GLN241 4.5 28.9 1.0 NE2 B:GLN241 4.6 31.8 1.0 CB B:GLU39 4.8 14.6 1.0 CG B:LEU243 4.9 18.2 1.0

Zinc binding site 5 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


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 (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3005 b:27.4 occ:1.00 O B:HOH3438 2.0 30.0 1.0 O B:HOH3439 2.1 39.1 1.0 ZN B:ZN3006 3.2 22.1 1.0 OG B:SER165 3.8 18.8 1.0 OE2 B:GLU163 3.8 20.0 1.0 CB B:SER165 3.8 13.5 1.0 O B:HOH3013 4.2 16.3 1.0 O B:HOH3129 4.2 33.0 1.0 CA B:SER165 4.3 14.5 1.0 OE1 B:GLU163 4.3 17.8 1.0 CD B:GLU163 4.4 17.4 1.0 O B:ALA162 4.5 17.1 1.0 O B:ARG160 4.7 21.9 1.0 N B:SER165 4.8 15.6 1.0 O B:HOH3284 4.9 46.0 1.0

Zinc binding site 6 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


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 (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3006 b:22.1 occ:1.00 OE1 B:GLU163 1.8 17.8 1.0 CD B:GLU163 2.4 17.4 1.0 OE2 B:GLU163 2.5 20.0 1.0 ZN B:ZN3005 3.2 27.4 1.0 CG B:GLU163 3.8 20.7 1.0 O B:HOH3438 4.0 30.0 1.0 N B:SER165 4.2 15.6 1.0 CB B:GLU163 4.5 21.3 1.0 CB B:SER165 4.6 13.5 1.0 CA B:SER165 4.7 14.5 1.0 O B:ALA162 4.7 17.1 1.0 CA B:GLU163 4.7 19.7 1.0 C B:PRO164 4.9 17.4 1.0 CA B:PRO164 5.0 18.9 1.0

C.Kasper, M.-L.Lunn, T.Liljefors, E.Gouaux, J.Egebjerg, J.S.Kastrup. GLUR2 Ligand-Binding Core Complexes: Importance of the Isoxazolol Moiety and 5-Substituent For the Binding Mode of Ampa-Type Agonists Febs Lett. V. 531 173 2002.
ISSN: ISSN 0014-5793
PubMed: 12417307
DOI: 10.1016/S0014-5793(02)03496-8