Zinc in PDB 9b36: Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map.

The structure of Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map. also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Fluorine	(F)	4 atoms

The binding sites of Zinc atom in the Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map. (pdb code 9b36). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map., PDB code: 9b36:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map. 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 4 in the Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map. 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

Zinc binding site 3 out of 4 in the Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map. within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1001 b:118.8 occ:1.00 OD2 G:ASP10 2.2 81.1 1.0 OD1 G:ASP19 2.2 84.8 1.0 OE1 G:GLU8 2.4 74.6 1.0 NE2 G:HIS24 2.4 80.6 1.0 CG G:ASP19 2.4 84.8 1.0 CE1 G:HIS24 2.6 80.6 1.0 OD2 G:ASP19 2.6 84.8 1.0 CD G:GLU8 2.6 74.6 1.0 OE2 G:GLU8 2.7 74.6 1.0 CG G:ASP10 2.9 81.1 1.0 CB G:ASP10 3.0 81.1 1.0 CA G:CA1002 3.3 126.3 1.0 CB G:ASP19 3.6 84.8 1.0 CD2 G:HIS24 3.7 80.6 1.0 CG G:GLU8 3.8 74.6 1.0 ND1 G:HIS24 3.8 80.6 1.0 OD1 G:ASP10 4.1 81.1 1.0 CG G:HIS24 4.4 80.6 1.0 CB G:GLU8 4.4 74.6 1.0 CA G:ASP10 4.5 81.1 1.0 CD1 G:LEU230 4.5 79.1 1.0 CA G:ASP19 4.5 84.8 1.0 OD1 G:ASN14 4.6 88.8 1.0 OG G:SER34 4.8 77.6 1.0 O G:TYR12 4.9 88.0 1.0

Zinc binding site 4 out of 4 in the Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Open State of Kainate Receptor GLUK2 in Complex with Agonist Glutamate and Positive Allosteric Modulator BPAM344 Bound to Two Concanavalin A Dimers. Composite Map. within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn1001 b:94.2 occ:1.00 OD1 H:ASP19 2.1 62.8 1.0 OD2 H:ASP10 2.2 65.5 1.0 NE2 H:HIS24 2.3 61.4 1.0 CE1 H:HIS24 2.4 61.4 1.0 CG H:ASP19 2.5 62.8 1.0 CB H:ASP10 2.6 65.5 1.0 CG H:ASP10 2.8 65.5 1.0 OD2 H:ASP19 2.9 62.8 1.0 OE2 H:GLU8 3.0 69.5 1.0 CD H:GLU8 3.3 69.5 1.0 CB H:ASP19 3.5 62.8 1.0 OE1 H:GLU8 3.6 69.5 1.0 CD2 H:HIS24 3.6 61.4 1.0 ND1 H:HIS24 3.6 61.4 1.0 OD1 H:ASP10 4.0 65.5 1.0 CA H:ASP10 4.1 65.5 1.0 CG H:GLU8 4.2 69.5 1.0 CG H:HIS24 4.3 61.4 1.0 CA H:ASP19 4.4 62.8 1.0 CA H:CA1002 4.6 102.1 1.0 O H:TYR12 4.6 65.3 1.0 N H:ASP10 4.7 65.5 1.0 C H:ASP10 4.8 65.5 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