Zinc in PDB 6f28: Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A

The structure of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A, PDB code: 6f28 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)	28.37 / 2.40
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	131.039, 56.214, 87.189, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.2

The structure of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A (pdb code 6f28). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A, PDB code: 6f28:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:49.3 occ:1.00 OE2 A:GLU196 1.8 62.8 1.0 NZ A:LYS248 2.3 52.8 1.0 CD A:GLU196 2.6 54.5 1.0 OE1 A:GLU196 2.8 58.4 1.0 CE A:LYS248 3.6 57.4 1.0 CG A:GLU196 4.0 53.2 1.0 CD A:LYS248 4.6 55.5 1.0 NE2 A:GLN200 4.8 99.7 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:53.2 occ:1.00 OE2 A:GLU98 1.9 53.1 1.0 OD1 B:ASP242 1.9 51.6 1.0 ND1 B:HIS245 2.0 58.3 1.0 ND1 A:HIS95 2.1 56.3 1.0 OD2 B:ASP242 2.4 47.5 1.0 CG B:ASP242 2.4 44.5 1.0 CE1 A:HIS95 2.9 52.9 1.0 CD A:GLU98 2.9 44.0 1.0 CG B:HIS245 2.9 50.6 1.0 CE1 B:HIS245 3.0 56.3 1.0 OE1 A:GLU98 3.2 43.4 1.0 CG A:HIS95 3.2 53.3 1.0 CB B:HIS245 3.2 43.7 1.0 CB A:HIS95 3.7 48.5 1.0 CA A:HIS95 3.8 43.5 1.0 O A:HOH402 3.8 50.1 1.0 CB B:ASP242 3.9 45.1 1.0 CD2 B:HIS245 4.0 50.7 1.0 NE2 B:HIS245 4.0 54.0 1.0 NE2 A:HIS95 4.1 53.8 1.0 CG A:GLU98 4.2 41.1 1.0 CD2 A:HIS95 4.3 54.8 1.0 O B:HOH414 4.3 59.9 1.0 CB A:GLU98 4.6 40.6 1.0 N A:HIS95 4.7 43.1 1.0 CA B:ASP242 4.7 43.2 1.0 CA B:HIS245 4.8 39.5 1.0 O A:HIS95 4.8 40.4 1.0 O B:ASP242 4.8 39.7 1.0 C A:HIS95 4.8 44.0 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:47.7 occ:0.11 ND1 B:HIS82 2.1 0.8 1.0 O B:HOH401 2.5 64.8 1.0 CG B:HIS82 2.7 0.9 1.0 CB B:HIS82 2.9 0.2 1.0 CE1 B:HIS82 3.2 0.9 1.0 CD2 B:HIS82 3.9 0.7 1.0 NE2 B:HIS82 4.1 0.8 1.0 CA B:HIS82 4.4 84.9 1.0 O B:ASP81 4.8 97.0 1.0 O B:HIS82 4.8 74.4 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:80.0 occ:0.71 NE2 B:HIS95 2.1 0.6 1.0 NZ B:LYS99 2.3 0.1 1.0 CE1 B:HIS95 2.4 0.9 1.0 CE B:LYS99 2.6 97.9 1.0 CD2 B:HIS95 3.4 0.3 1.0 ND1 B:HIS95 3.7 0.1 1.0 CD B:LYS99 4.1 96.1 1.0 CG B:HIS95 4.1 0.1 1.0 CG B:LYS99 4.9 89.8 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:41.4 occ:0.18 OE1 B:GLU44 2.0 70.3 1.0 NZ B:LYS243 2.0 85.6 1.0 CD B:GLU44 2.9 68.5 1.0 CE B:LYS243 3.3 85.3 1.0 OE2 B:GLU44 3.3 70.5 1.0 CD B:LYS243 3.5 78.7 1.0 CG B:GLU44 4.3 64.5 1.0 CD2 B:LEU238 4.3 46.2 1.0 OE2 B:GLU241 4.6 90.3 1.0 CB B:GLU44 4.6 59.1 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