Zinc in PDB 5oew: Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538

The structure of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538, PDB code: 5oew was solved by A.P.Larsen, K.A.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.52 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.702, 164.374, 47.328, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 18.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 (pdb code 5oew). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538, PDB code: 5oew:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538


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 GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:21.3 occ:0.87 OE1 C:GLU166 2.0 27.7 1.0 O A:HOH546 2.1 27.9 1.0 NE2 A:HIS46 2.1 24.1 1.0 OE1 A:GLU42 2.1 22.6 1.0 OE2 C:GLU166 2.6 29.4 1.0 CD C:GLU166 2.6 28.2 1.0 CD A:GLU42 2.9 21.2 1.0 CD2 A:HIS46 3.1 22.1 1.0 CE1 A:HIS46 3.1 25.5 1.0 OE2 A:GLU42 3.2 21.4 1.0 CD2 A:LEU241 4.1 23.0 1.0 CG C:GLU166 4.1 26.8 1.0 ND1 A:HIS46 4.2 24.6 1.0 CG A:HIS46 4.2 22.6 1.0 CG A:GLU42 4.3 18.9 1.0 N C:SER168 4.4 19.3 1.0 O C:ALA165 4.6 20.6 1.0 O C:HOH542 4.6 32.6 1.0 CB A:GLU42 4.7 15.6 1.0 CB C:GLU166 4.7 24.9 1.0 CB C:SER168 4.8 18.6 1.0 CA C:SER168 4.8 18.4 1.0 CD2 A:LEU246 4.9 36.1 1.0 CA C:GLU166 4.9 23.4 1.0 C C:PRO167 5.0 22.3 1.0

Zinc binding site 2 out of 18 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538


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 GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:0.3 occ:1.00 OD1 A:ASP126 2.2 48.8 1.0 CG A:ASP126 3.0 40.8 1.0 OD2 A:ASP126 3.1 39.9 1.0 OG A:SER123 4.2 29.3 1.0 CB A:ASP126 4.4 32.5 1.0 OE1 A:GLU122 4.5 59.7 1.0 NZ A:LYS129 4.7 70.7 1.0 CA A:ASP126 4.9 28.9 1.0 N A:ASP126 5.0 28.2 1.0

Zinc binding site 3 out of 18 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538


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 GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:84.0 occ:0.80 O A:HOH411 2.2 84.2 1.0 O A:HOH407 2.2 58.6 1.0 OE1 A:GLU201 4.0 50.6 1.0 OE2 A:GLU201 4.1 43.3 1.0 O A:LYS210 4.2 30.0 1.0 CD A:GLU201 4.5 42.9 1.0 CB A:LYS210 4.7 25.3 1.0 O A:HOH548 4.9 50.6 1.0 CD A:LYS210 5.0 35.5 1.0

Zinc binding site 4 out of 18 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538


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 GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn903 b:48.1 occ:0.81 NE2 B:HIS46 2.2 38.5 1.0 O B:HOH1140 2.2 65.4 1.0 OE1 B:GLU42 2.3 33.6 1.0 O B:HOH1063 2.3 43.3 1.0 CD2 B:HIS46 3.1 34.3 1.0 CE1 B:HIS46 3.2 42.3 1.0 CD B:GLU42 3.2 32.9 1.0 O B:HOH1002 3.3 57.3 1.0 CE B:LYS45 3.4 48.2 1.0 OE2 B:GLU42 3.4 39.3 1.0 NZ B:LYS45 3.5 51.8 1.0 CD2 B:LEU241 4.1 22.2 1.0 NE2 B:GLN244 4.2 39.2 1.0 CG B:HIS46 4.2 36.1 1.0 ND1 B:HIS46 4.2 42.2 1.0 CG B:GLU42 4.6 26.8 1.0 CD B:LYS45 4.8 43.7 1.0 CB B:GLU42 4.9 26.4 1.0

Zinc binding site 5 out of 18 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538


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 GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn904 b:83.2 occ:1.00 O B:HOH1017 2.3 47.0 1.0 OD2 B:ASP139 2.4 48.3 1.0 CG B:ASP139 3.1 37.3 1.0 OD1 B:ASP139 3.2 33.5 1.0 O B:HOH1042 4.1 51.2 1.0 CB B:ASP139 4.4 29.5 1.0 NZ B:LYS144 4.4 34.7 1.0 O B:HOH1130 4.5 48.4 1.0 OG B:SER140 5.0 32.4 1.0

Zinc binding site 6 out of 18 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538


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 GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn905 b:72.1 occ:1.00 OD1 B:ASP156 2.0 77.3 1.0 O B:HOH1052 2.1 59.5 1.0 O B:HOH1133 2.3 71.6 1.0 O B:HOH1124 2.7 60.2 1.0 CG B:ASP156 3.0 57.3 1.0 OD2 B:ASP156 3.3 57.3 1.0 O B:HOH1067 3.7 77.9 1.0 O B:HOH1029 3.8 36.4 1.0 CB B:ASP156 4.3 45.6 1.0 OG1 B:THR160 4.9 42.8 1.0 O B:ASP156 4.9 33.1 1.0 NH1 B:ARG163 4.9 65.1 1.0 CA B:ASP156 5.0 36.0 1.0 O B:SER150 5.0 46.0 1.0

Zinc binding site 7 out of 18 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538


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 GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn906 b:24.9 occ:0.84 O B:HOH1122 1.8 23.8 1.0 OXT B:ACT909 1.9 29.2 1.0 OD1 B:ASP65 2.1 24.4 1.0 O B:ACT909 2.5 51.0 1.0 C B:ACT909 2.6 40.5 1.0 CG B:ASP65 2.8 24.8 1.0 OD2 B:ASP65 2.8 27.1 1.0 O B:HOH1008 3.5 42.1 1.0 CH3 B:ACT909 4.1 41.1 1.0 OD1 B:ASP67 4.1 69.0 1.0 CB B:ASP65 4.3 22.8 1.0 CB B:ASP67 4.4 42.9 1.0 CG B:ASP67 4.5 58.1 1.0 N B:ASP67 4.9 37.6 1.0

Zinc binding site 8 out of 18 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn907 b:86.7 occ:1.00 ND1 B:HIS46 2.5 42.2 1.0 O B:HOH1158 2.8 42.6 1.0 CG B:HIS46 3.4 36.1 1.0 CE1 B:HIS46 3.5 42.3 1.0 CB B:HIS46 3.5 33.3 1.0 CE B:LYS240 3.9 49.4 1.0 CD B:LYS240 4.0 40.9 1.0 CA B:HIS46 4.1 34.0 1.0 O B:HIS46 4.1 38.7 1.0 O B:HOH1151 4.3 37.0 1.0 CD2 B:HIS46 4.5 34.3 1.0 C B:HIS46 4.6 34.6 1.0 NE2 B:HIS46 4.6 38.5 1.0 CG B:LYS240 5.0 31.1 1.0

Zinc binding site 9 out of 18 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn908 b:0.0 occ:0.86 O B:HOH1006 2.2 42.9 1.0 O B:HOH1007 2.3 58.7 1.0 OE2 B:GLU201 3.9 50.0 1.0 OE1 B:GLU201 4.0 40.0 1.0 O B:LYS210 4.1 29.3 1.0 CD B:GLU201 4.4 42.5 1.0

Zinc binding site 10 out of 18 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Positive Allosteric Modulator BPAM538 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:31.5 occ:0.64 O C:HOH510 2.0 28.5 1.0 ND1 C:HIS46 2.2 20.1 1.0 O C:HOH580 2.5 35.1 1.0 O C:HOH584 2.8 31.0 1.0 CE1 C:HIS46 3.2 20.9 1.0 CG C:HIS46 3.2 18.3 1.0 CB C:HIS46 3.5 17.2 1.0 CA C:HIS46 4.0 18.1 1.0 O C:HIS46 4.2 23.2 1.0 NE2 C:HIS46 4.3 23.2 1.0 CD2 C:HIS46 4.3 19.4 1.0 C C:HIS46 4.6 19.7 1.0 CG C:LYS240 4.7 27.7 1.0 CE C:LYS240 4.8 44.8 1.0

E.Goffin, T.Drapier, A.P.Larsen, P.Geubelle, C.P.Ptak, S.Laulumaa, K.Rovinskaja, J.Gilissen, P.Tullio, L.Olsen, K.Frydenvang, B.Pirotte, J.Hanson, R.E.Oswald, J.S.Kastrup, P.Francotte. 7-Phenoxy-Substituted 3,4-Dihydro-2H-1,2,4-Benzothiadiazine 1,1-Dioxides As Positive Allosteric Modulators of Alpha-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid (Ampa) Receptors with Nanomolar Potency. J. Med. Chem. V. 61 251 2018.
ISSN: ISSN 1520-4804
PubMed: 29256599
DOI: 10.1021/ACS.JMEDCHEM.7B01323