Calcium in PDB 9b33: 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 One Cona Dimer. Type II 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 One Cona Dimer. Type II 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 One Cona Dimer. Type II Interface Between GLUK2 Ligand-Binding Domain and Cona (pdb code 9b33). 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 One Cona Dimer. Type II Interface Between GLUK2 Ligand-Binding Domain and Cona, PDB code: 9b33:
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 One Cona Dimer. Type II 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 One Cona Dimer. Type II Interface Between GLUK2 Ligand-Binding Domain and Cona within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1002 b:109.1 occ:1.00 OD1 E:ASN14 2.6 162.3 1.0 O E:ARG228 2.6 155.7 1.0 OD1 E:ASP208 2.9 172.4 1.0 CA E:ARG228 2.9 155.7 1.0 C E:ARG228 3.1 155.7 1.0 CG E:ASN14 3.3 162.3 1.0 CB E:ARG228 3.4 155.7 1.0 ND2 E:ASN14 3.5 162.3 1.0 CG E:ASP208 3.8 172.4 1.0 OD2 E:ASP208 4.1 172.4 1.0 N E:ARG228 4.2 155.7 1.0 N E:LEU229 4.4 147.7 1.0 OD2 E:ASP10 4.4 156.6 1.0 O E:GLY227 4.4 156.9 1.0 CB E:ASN14 4.6 162.3 1.0 OD1 E:ASP10 4.6 156.6 1.0 OD2 E:ASP19 4.6 160.0 1.0 C E:GLY227 4.6 156.9 1.0 O E:ASP208 4.7 172.4 1.0 CG E:ARG228 4.7 155.7 1.0 N E:LEU230 4.8 142.4 1.0 CD1 E:ILE17 4.8 161.1 1.0 CG E:ASP10 4.9 156.6 1.0 CD2 E:TYR12 4.9 154.6 1.0 O E:TYR12 5.0 154.6 1.0 CB E:LEU230 5.0 142.4 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 One Cona Dimer. Type II 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 One Cona Dimer. Type II Interface Between GLUK2 Ligand-Binding Domain and Cona within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1002 b:104.0 occ:1.00 OD1 F:ASN14 2.5 127.7 1.0 O F:TYR12 2.5 134.4 1.0 OD1 F:ASP10 2.6 115.8 1.0 ND2 F:ASN14 2.6 127.7 1.0 OD1 F:ASP208 2.7 150.6 1.0 CG F:ASN14 2.8 127.7 1.0 CB F:TYR12 2.9 134.4 1.0 C F:TYR12 3.3 134.4 1.0 OD2 F:ASP10 3.4 115.8 1.0 CG F:ASP10 3.4 115.8 1.0 CA F:TYR12 3.4 134.4 1.0 N F:TYR12 3.5 134.4 1.0 CG F:ASP208 3.9 150.6 1.0 CG F:TYR12 3.9 134.4 1.0 CD2 F:TYR12 3.9 134.4 1.0 CB F:ASN14 4.2 127.7 1.0 N F:ASN14 4.3 127.7 1.0 CA F:ASP208 4.4 150.6 1.0 N F:PRO13 4.5 128.3 1.0 O F:ASP208 4.5 150.6 1.0 CA F:ASN14 4.7 127.7 1.0 OD2 F:ASP208 4.7 150.6 1.0 CB F:ARG228 4.7 149.7 1.0 CA F:ARG228 4.7 149.7 1.0 CB F:ASP208 4.7 150.6 1.0 C F:THR11 4.8 132.0 1.0 CB F:ASP10 4.8 115.8 1.0 C F:PRO13 4.9 128.3 1.0 N F:THR11 4.9 132.0 1.0 C F:ASP208 4.9 150.6 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