Calcium 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:

Zinc

(Zn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca1002 b:129.4 occ:1.00 OD2 E:ASP10 2.5 92.3 1.0 OD1 E:ASN14 2.5 98.1 1.0 OD2 E:ASP19 2.9 93.1 1.0 CG E:ASP10 3.0 92.3 1.0 OD1 E:ASP10 3.1 92.3 1.0 CD1 E:LEU230 3.2 85.3 1.0 ZN E:ZN1001 3.6 123.2 1.0 CG E:ASN14 3.6 98.1 1.0 O E:ARG228 3.9 95.0 1.0 OD1 E:ASP208 4.0 99.8 1.0 OE1 E:GLU8 4.0 87.5 1.0 CG E:ASP19 4.0 93.1 1.0 CB E:ASP10 4.1 92.3 1.0 O E:TYR12 4.3 97.4 1.0 CB E:ASN14 4.4 98.1 1.0 CG E:LEU230 4.4 85.3 1.0 ND2 E:ASN14 4.4 98.1 1.0 CB E:LEU230 4.5 85.3 1.0 O E:ASP208 4.6 99.8 1.0 OD1 E:ASP19 4.6 93.1 1.0 C E:ARG228 4.6 95.0 1.0 CA E:ARG228 4.7 95.0 1.0 CD1 E:ILE17 4.9 96.8 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca1002 b:87.2 occ:1.00 OD1 F:ASP10 2.5 65.3 1.0 OD2 F:ASP10 2.6 65.3 1.0 O F:TYR12 2.6 67.0 1.0 OD1 F:ASN14 2.6 72.1 1.0 CG F:ASP10 2.9 65.3 1.0 CB F:TYR12 3.0 67.0 1.0 C F:TYR12 3.3 67.0 1.0 CA F:TYR12 3.4 67.0 1.0 N F:TYR12 3.5 67.0 1.0 CG F:ASN14 3.8 72.1 1.0 OD2 F:ASP19 3.9 63.9 1.0 CG F:TYR12 4.0 67.0 1.0 CD2 F:TYR12 4.0 67.0 1.0 OD1 F:ASP208 4.0 78.9 1.0 CB F:ASP10 4.4 65.3 1.0 CA F:ARG228 4.5 80.4 1.0 N F:PRO13 4.6 63.6 1.0 ZN F:ZN1001 4.7 80.4 1.0 ND2 F:ASN14 4.7 72.1 1.0 CD1 F:LEU230 4.7 77.4 1.0 O F:ASP208 4.7 78.9 1.0 C F:THR11 4.7 68.9 1.0 N F:THR11 4.8 68.9 1.0 CB F:ASN14 4.8 72.1 1.0 CG F:ASP19 4.9 63.9 1.0 O F:ARG228 4.9 80.4 1.0 CA F:ASP208 4.9 78.9 1.0 CB F:ARG228 5.0 80.4 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