Potassium in PDB 6f29: Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A

The structure of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A, PDB code: 6f29 was solved by R.Venskutonyte, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.92 / 2.60
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.040, 68.040, 126.860, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.8

The structure of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Potassium atom in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A (pdb code 6f29). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A, PDB code: 6f29:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A within 5.0Å range: probe atom residue distance (Å) B Occ A:K302 b:72.1 occ:1.00 O A:SER24 2.8 40.3 1.0 O A:ARG26 2.9 36.8 1.0 O A:HOH423 3.1 37.8 1.0 O A:HOH404 3.7 56.6 1.0 C A:SER24 3.8 38.0 1.0 C A:ARG26 4.0 37.4 1.0 N A:SER24 4.4 32.7 1.0 O A:ASP25 4.5 44.3 1.0 C A:ASP25 4.5 44.9 1.0 CA A:SER24 4.5 32.8 1.0 CA A:THR27 4.6 37.6 1.0 N A:THR27 4.7 39.0 1.0 CB A:SER24 4.7 30.8 1.0 N A:ARG26 4.8 37.9 1.0 N A:ASP25 4.8 43.0 1.0 CA A:ASP25 4.9 43.7 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A within 5.0Å range: probe atom residue distance (Å) B Occ A:K303 b:68.0 occ:0.50 OG A:SER52 2.9 33.8 1.0 O A:HOH406 2.9 34.1 1.0 O A:ASN5 3.3 78.5 1.0 O A:HOH436 3.7 34.2 1.0 CB A:SER52 3.8 27.6 1.0 N A:SER52 4.0 25.9 1.0 C A:ASN5 4.3 78.3 1.0 OG A:SER7 4.4 39.2 1.0 O A:ARG6 4.4 42.4 1.0 C A:ARG6 4.5 45.6 1.0 CA A:SER52 4.5 24.8 1.0 N A:SER7 4.8 41.4 1.0 C A:PHE51 4.8 25.0 1.0 CA A:ARG6 4.8 57.2 1.0 CA A:PHE51 5.0 26.0 1.0 N A:ARG6 5.0 68.7 1.0

S.Brogi, M.Brindisi, S.Butini, G.U.Kshirsagar, S.Maramai, G.Chemi, S.Gemma, G.Campiani, E.Novellino, P.Fiorenzani, J.Pinassi, A.M.Aloisi, M.Gynther, R.Venskutonyte, L.Han, K.Frydenvang, J.S.Kastrup, D.S.Pickering. ( S)-2-Amino-3-(5-Methyl-3-Hydroxyisoxazol-4-Yl)Propanoic Acid (Ampa) and Kainate Receptor Ligands: Further Exploration of Bioisosteric Replacements and Structural and Biological Investigation. J. Med. Chem. V. 61 2124 2018.
ISSN: ISSN 1520-4804
PubMed: 29451794
DOI: 10.1021/ACS.JMEDCHEM.8B00099