Zinc in PDB 8qez: Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution

The structure of Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution, PDB code: 8qez was solved by J.Dorosz, S.Laulumaa, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.17 / 1.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.316, 163.416, 47.466, 90, 90, 90
R / Rfree (%)	16.8 / 19.5

The structure of Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Arsenic	(As)	1 atom

The binding sites of Zinc atom in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution (pdb code 8qez). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution, PDB code: 8qez:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:23.1 occ:1.00 OE2 A:GLU24 1.9 37.5 1.0 NE2 A:HIS23 2.2 24.8 1.0 HG2 A:GLU24 2.8 55.2 1.0 CD A:GLU24 2.9 50.2 1.0 CD2 A:HIS23 3.0 26.4 1.0 HD2 A:HIS23 3.1 31.7 1.0 CG A:GLU24 3.2 46.0 1.0 CE1 A:HIS23 3.3 28.7 1.0 HG3 A:GLU24 3.4 55.2 1.0 HE1 A:HIS23 3.5 34.5 1.0 OE1 A:GLU24 4.0 51.0 1.0 CG A:HIS23 4.2 24.6 1.0 ND1 A:HIS23 4.3 24.0 1.0 SD A:MET19 4.7 26.1 1.0 CB A:GLU24 4.7 35.3 1.0 O A:HOH560 4.9 28.1 1.0 H A:GLU24 5.0 31.4 1.0 HA A:GLU24 5.0 33.4 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:36.2 occ:0.67 O A:HOH407 2.1 41.9 1.0 OE1 A:GLU42 2.2 33.6 1.0 NE2 A:HIS46 2.3 39.4 1.0 O A:HOH590 2.3 49.4 1.0 O A:HOH592 2.6 46.4 1.0 CD2 A:HIS46 3.2 32.6 1.0 CD A:GLU42 3.2 31.5 1.0 HD2 A:HIS46 3.2 39.1 1.0 CE1 A:HIS46 3.3 48.2 1.0 HD21 A:LEU241 3.3 33.4 1.0 HE3 A:LYS45 3.3 60.2 1.0 HZ1 A:LYS45 3.4 70.0 1.0 HE2 A:LYS45 3.4 60.2 1.0 HE1 A:HIS46 3.5 57.9 1.0 OE2 A:GLU42 3.6 42.9 1.0 HD23 A:LEU241 3.7 33.4 1.0 CE A:LYS45 3.7 50.1 1.0 CD2 A:LEU241 3.8 27.8 1.0 HD22 A:LEU241 3.9 33.4 1.0 NZ A:LYS45 4.0 58.3 1.0 OE1 A:GLN244 4.2 41.5 1.0 HB3 A:GLU42 4.2 27.9 1.0 HE22 A:GLN244 4.3 55.8 1.0 CG A:HIS46 4.3 34.8 1.0 ND1 A:HIS46 4.4 45.1 1.0 CG A:GLU42 4.5 29.1 1.0 HZ3 A:LYS45 4.6 70.0 1.0 HZ2 A:LYS45 4.6 70.0 1.0 HG A:LEU246 4.6 35.9 1.0 HA A:GLU42 4.7 23.7 1.0 CB A:GLU42 4.8 23.2 1.0 HG3 A:GLU42 4.9 35.0 1.0 NE2 A:GLN244 5.0 46.5 1.0 CD A:GLN244 5.0 46.3 1.0 HB3 A:LYS45 5.0 37.4 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:27.7 occ:0.90 OXT A:ACT309 1.8 47.4 0.9 O A:ACT307 2.0 38.3 0.9 OD2 A:ASP65 2.0 28.7 1.0 O A:ACT309 2.1 43.9 0.9 C A:ACT309 2.1 36.9 0.9 OXT A:ACT307 2.3 43.6 0.9 C A:ACT307 2.4 39.8 0.9 CG A:ASP65 2.8 35.6 1.0 OD1 A:ASP65 2.8 35.2 1.0 HB2 A:ASP67 3.6 47.8 1.0 CH3 A:ACT309 3.7 59.3 0.9 CH3 A:ACT307 3.9 40.1 0.9 HG23 A:THR68 4.0 45.0 1.0 H3 A:ACT309 4.1 71.2 0.9 H2 A:ACT309 4.1 71.2 0.9 H1 A:ACT309 4.2 71.2 0.9 OD2 A:ASP67 4.2 49.4 1.0 CB A:ASP65 4.2 30.6 1.0 H2 A:ACT307 4.3 48.2 0.9 H1 A:ACT307 4.3 48.2 0.9 H A:ASP67 4.3 44.3 1.0 HB2 A:ASP65 4.4 36.7 1.0 H3 A:ACT307 4.4 48.2 0.9 H A:THR68 4.5 45.1 1.0 CB A:ASP67 4.5 39.8 1.0 HB3 A:ASP65 4.7 36.7 1.0 O A:HOH417 4.8 39.4 1.0 CG A:ASP67 4.9 47.7 1.0 CG2 A:THR68 4.9 37.5 1.0 HA A:ASP65 4.9 37.2 1.0 HG21 A:THR68 4.9 45.0 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:96.4 occ:0.79 OD1 A:ASP156 2.1 55.4 1.0 O A:HOH604 2.5 55.3 1.0 CG A:ASP156 3.3 47.5 1.0 O A:HOH478 3.6 34.3 1.0 HD1 A:TRP159 3.8 43.9 1.0 OD2 A:ASP156 4.1 62.5 1.0 HA A:ASP156 4.3 51.4 1.0 OG1 A:THR160 4.3 47.4 1.0 HG1 A:THR160 4.3 56.8 1.0 HB2 A:ASP156 4.3 52.5 1.0 CB A:ASP156 4.4 43.8 1.0 HH22 A:ARG163 4.6 91.8 1.0 O A:ASP156 4.6 41.1 1.0 CD1 A:TRP159 4.7 36.6 1.0 CA A:ASP156 4.8 42.8 1.0 NH2 A:ARG163 4.8 76.5 1.0 HZ2 A:LYS151 4.9 80.5 1.0 O A:SER150 4.9 44.5 1.0 HB3 A:TRP159 5.0 43.1 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:18.6 occ:1.00 OE1 C:GLU166 1.9 20.0 1.0 OE1 B:GLU42 2.0 17.2 1.0 O2 C:CAC304 2.0 18.9 0.9 NE2 B:HIS46 2.2 19.0 1.0 CD C:GLU166 2.6 27.1 1.0 OE2 C:GLU166 2.6 26.4 1.0 CD B:GLU42 2.9 16.8 1.0 CD2 B:HIS46 3.0 19.0 1.0 HD2 B:HIS46 3.1 22.8 1.0 OE2 B:GLU42 3.2 18.1 1.0 CE1 B:HIS46 3.2 24.1 1.0 HD21 B:LEU241 3.3 28.1 1.0 AS C:CAC304 3.3 26.0 0.9 HE1 B:HIS46 3.4 29.0 1.0 H11 C:CAC304 3.7 26.9 0.9 H21 C:CAC304 3.7 27.2 0.9 H C:SER168 3.8 21.8 1.0 HB2 C:SER168 3.9 21.9 1.0 C1 C:CAC304 3.9 22.4 0.9 CD2 B:LEU241 4.0 23.4 1.0 C2 C:CAC304 4.0 22.6 0.9 HD22 B:LEU241 4.0 28.1 1.0 H12 C:CAC304 4.0 26.9 0.9 CG C:GLU166 4.1 24.6 1.0 H23 C:CAC304 4.1 27.2 0.9 HB3 B:GLU42 4.2 17.9 1.0 HD23 B:LEU241 4.2 28.1 1.0 HA C:GLU166 4.2 21.7 1.0 CG B:HIS46 4.2 18.2 1.0 HA C:PRO167 4.2 23.1 1.0 N C:SER168 4.2 18.1 1.0 CG B:GLU42 4.3 15.4 1.0 ND1 B:HIS46 4.3 21.2 1.0 HG3 C:GLU166 4.5 29.6 1.0 HB3 C:GLU166 4.5 26.1 1.0 HA B:GLU42 4.5 18.9 1.0 HA C:SER168 4.5 19.0 1.0 HD22 B:LEU246 4.5 43.2 1.0 HG2 C:GLU166 4.6 29.6 1.0 HG3 B:GLU42 4.6 18.5 1.0 CB B:GLU42 4.7 14.9 1.0 HD3 B:LYS45 4.7 56.0 1.0 O C:ALA165 4.7 19.7 1.0 CB C:SER168 4.7 18.3 1.0 CB C:GLU166 4.7 21.8 1.0 CA C:SER168 4.7 15.8 1.0 O1 C:CAC304 4.8 24.8 0.9 H13 C:CAC304 4.9 26.9 0.9 HG2 B:GLU42 4.9 18.5 1.0 H22 C:CAC304 4.9 27.2 0.9 CA C:GLU166 4.9 18.1 1.0 C C:PRO167 4.9 17.8 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:19.0 occ:0.91 O C:HOH405 2.0 21.6 1.0 OE1 C:GLU42 2.0 20.0 1.0 NE2 C:HIS46 2.1 19.6 1.0 CD C:GLU42 2.9 21.8 1.0 CD2 C:HIS46 3.0 18.1 1.0 HD2 C:HIS46 3.1 21.8 1.0 CE1 C:HIS46 3.2 25.4 1.0 HZ3 C:LYS45 3.2 24.8 1.0 OE2 C:GLU42 3.2 22.9 1.0 HD21 C:LEU241 3.3 22.8 1.0 HE1 C:HIS46 3.4 30.5 1.0 HD23 C:LEU241 3.4 22.8 1.0 HE2 C:LYS45 3.5 26.1 1.0 HE3 C:LYS45 3.6 26.1 1.0 CD2 C:LEU241 3.7 19.0 1.0 HD22 C:LEU241 3.7 22.8 1.0 OE1 C:GLN244 3.7 31.0 1.0 HE22 C:GLN244 3.8 38.2 1.0 CE C:LYS45 3.9 21.8 1.0 NZ C:LYS45 3.9 20.6 1.0 HB3 C:GLU42 4.0 19.2 1.0 CG C:HIS46 4.2 19.9 1.0 ND1 C:HIS46 4.2 28.9 1.0 CG C:GLU42 4.3 18.7 1.0 HZ1 C:LYS45 4.4 24.8 1.0 NE2 C:GLN244 4.4 31.9 1.0 CD C:GLN244 4.5 29.5 1.0 HZ2 C:LYS45 4.5 24.8 1.0 HG C:LEU246 4.6 30.6 1.0 HG3 C:GLU42 4.6 22.4 1.0 CB C:GLU42 4.6 16.0 1.0 HA C:GLU42 4.7 20.1 1.0 HG2 C:GLU42 4.9 22.4 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:58.0 occ:0.48 OD2 C:ASP156 2.3 43.9 1.0 O C:HOH486 3.0 26.7 1.0 HD1 C:TRP159 3.0 32.4 1.0 CG C:ASP156 3.3 37.9 1.0 HA C:ASP156 3.8 34.4 1.0 CD1 C:TRP159 3.9 27.0 1.0 OD1 C:ASP156 4.1 43.2 1.0 HB2 C:ASP156 4.1 33.4 1.0 HB3 C:TRP159 4.2 31.1 1.0 CB C:ASP156 4.2 27.8 1.0 HH11 C:ARG163 4.2 65.8 1.0 OG1 C:THR160 4.2 27.9 1.0 HH12 C:ARG163 4.3 65.8 1.0 O C:ASP156 4.3 26.8 1.0 CA C:ASP156 4.4 28.6 1.0 HG1 C:THR160 4.4 33.4 1.0 NH1 C:ARG163 4.5 54.8 1.0 O C:SER150 4.7 31.3 1.0 C C:ASP156 4.7 26.1 1.0 HE1 C:TRP159 4.8 30.3 1.0 NE1 C:TRP159 4.8 25.2 1.0 CG C:TRP159 4.8 23.1 1.0 CB C:TRP159 5.0 25.9 1.0 H C:THR160 5.0 26.6 1.0

P.Francotte, Y.Bay, E.Goffin, T.Colson, C.Lesenfants, J.Dorosz, S.Laulumaa, P.Fraikin, P.De Tullio, C.Beaufour, I.Botez, D.S.Pickering, K.Frydenvang, L.Danober, A.S.Kristensen, J.S.Kastrup, B.Pirotte. Exploring Thienothiadiazine Dioxides As Isosteric Analogues of Benzo- and Pyridothiadiazine Dioxides in the Search of New Ampa and Kainate Receptor Positive Allosteric Modulators. Eur.J.Med.Chem. V. 264 16036 2023.
ISSN: ISSN 0223-5234
PubMed: 38101041
DOI: 10.1016/J.EJMECH.2023.116036