Zinc in PDB 9b34: Structure of Concanavalin A (Cona) Dimer From the Open-State Structure of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Cona Dimers. Type I Interface Between GLUK2 Ligand-Binding Domain and Cona

The structure of Structure of Concanavalin A (Cona) Dimer From the Open-State Structure of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Cona Dimers. Type I Interface Between GLUK2 Ligand-Binding Domain and Cona also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Structure of Concanavalin A (Cona) Dimer From the Open-State Structure of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Cona Dimers. Type I Interface Between GLUK2 Ligand-Binding Domain and Cona (pdb code 9b34). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Concanavalin A (Cona) Dimer From the Open-State Structure of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Cona Dimers. Type I Interface Between GLUK2 Ligand-Binding Domain and Cona, PDB code: 9b34:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Concanavalin A (Cona) Dimer From the Open-State Structure of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Cona Dimers. Type I Interface Between GLUK2 Ligand-Binding Domain and Cona


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Concanavalin A (Cona) Dimer From the Open-State Structure of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Cona Dimers. Type I Interface Between GLUK2 Ligand-Binding Domain and Cona within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:123.2 occ:1.00 OD2 E:ASP10 2.1 92.3 1.0 OD1 E:ASP19 2.1 93.1 1.0 NE2 E:HIS24 2.3 92.2 1.0 CG E:ASP19 2.4 93.1 1.0 CE1 E:HIS24 2.4 92.2 1.0 OE1 E:GLU8 2.6 87.5 1.0 OD2 E:ASP19 2.6 93.1 1.0 OE2 E:GLU8 2.7 87.5 1.0 CD E:GLU8 2.8 87.5 1.0 CG E:ASP10 2.9 92.3 1.0 CB E:ASP10 2.9 92.3 1.0 CB E:ASP19 3.5 93.1 1.0 CA E:CA1002 3.6 129.4 1.0 CD2 E:HIS24 3.6 92.2 1.0 ND1 E:HIS24 3.7 92.2 1.0 CG E:GLU8 3.9 87.5 1.0 OD1 E:ASP10 4.1 92.3 1.0 CG E:HIS24 4.3 92.2 1.0 CA E:ASP19 4.4 93.1 1.0 CA E:ASP10 4.4 92.3 1.0 CB E:GLU8 4.5 87.5 1.0 OD1 E:ASN14 4.6 98.1 1.0 CD1 E:LEU230 4.7 85.3 1.0 O E:TYR12 4.8 97.4 1.0 OG E:SER34 4.8 91.3 1.0

Zinc binding site 2 out of 2 in the Structure of Concanavalin A (Cona) Dimer From the Open-State Structure of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Cona Dimers. Type I Interface Between GLUK2 Ligand-Binding Domain and Cona


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Concanavalin A (Cona) Dimer From the Open-State Structure of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Cona Dimers. Type I Interface Between GLUK2 Ligand-Binding Domain and Cona within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1001 b:80.4 occ:1.00 OD2 F:ASP10 2.2 65.3 1.0 OD1 F:ASP19 2.2 63.9 1.0 NE2 F:HIS24 2.3 61.4 1.0 CE1 F:HIS24 2.4 61.4 1.0 CB F:ASP10 2.6 65.3 1.0 CG F:ASP19 2.6 63.9 1.0 CG F:ASP10 2.7 65.3 1.0 OD2 F:ASP19 2.9 63.9 1.0 OE2 F:GLU8 3.0 68.4 1.0 CD F:GLU8 3.3 68.4 1.0 OE1 F:GLU8 3.5 68.4 1.0 CD2 F:HIS24 3.6 61.4 1.0 CB F:ASP19 3.6 63.9 1.0 ND1 F:HIS24 3.7 61.4 1.0 OD1 F:ASP10 4.0 65.3 1.0 CA F:ASP10 4.1 65.3 1.0 CG F:GLU8 4.1 68.4 1.0 CG F:HIS24 4.3 61.4 1.0 CA F:ASP19 4.5 63.9 1.0 N F:ASP10 4.6 65.3 1.0 O F:TYR12 4.7 67.0 1.0 CA F:CA1002 4.7 87.2 1.0 C F:ASP10 4.8 65.3 1.0 CB F:GLU8 5.0 68.4 1.0

S.P.Gangwar, M.V.Yelshanskaya, K.D.Nadezhdin, L.Y.Yen, T.P.Newton, M.Aktolun, M.G.Kurnikova, A.I.Sobolevsky. Kainate Receptor Channel Opening and Gating Mechanism Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-024-07475-0