Sodium in PDB 8ss9: Structure of Lbd-Tmd of Ampa Receptor GLUA2 in Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State)

The structure of Structure of Lbd-Tmd of Ampa Receptor GLUA2 in Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State) also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Sodium atom in the Structure of Lbd-Tmd of Ampa Receptor GLUA2 in Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State) (pdb code 8ss9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Lbd-Tmd of Ampa Receptor GLUA2 in Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State), PDB code: 8ss9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Lbd-Tmd of Ampa Receptor GLUA2 in Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Lbd-Tmd of Ampa Receptor GLUA2 in Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1108 b:36.8 occ:1.00 OG1 C:THR625 3.2 17.2 1.0 OG1 A:THR625 3.4 21.0 1.0 OG1 D:THR625 3.7 29.2 1.0 OG1 B:THR625 3.9 20.0 1.0 O C:ALA621 3.9 11.4 1.0 O A:ALA621 4.0 14.1 1.0 CB C:THR625 4.2 17.2 1.0 CB A:THR625 4.2 21.0 1.0 O D:ALA621 4.3 22.2 1.0 CG2 C:THR625 4.3 17.2 1.0 O B:ALA621 4.3 15.1 1.0 CG2 A:THR625 4.3 21.0 1.0 CB C:ALA621 4.4 11.4 1.0 CB D:ALA621 4.4 22.2 1.0 CB B:ALA621 4.4 15.1 1.0 C C:ALA621 4.4 11.4 1.0 C A:ALA621 4.5 14.1 1.0 CB A:ALA621 4.5 14.1 1.0 CB D:THR625 4.7 29.2 1.0 C B:ALA621 4.7 15.1 1.0 C D:ALA621 4.7 22.2 1.0 CG2 D:THR625 4.7 29.2 1.0 CB B:THR625 4.8 20.0 1.0 CG2 B:THR625 4.9 20.0 1.0 CA C:ALA621 5.0 11.4 1.0

Sodium binding site 2 out of 2 in the Structure of Lbd-Tmd of Ampa Receptor GLUA2 in Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Lbd-Tmd of Ampa Receptor GLUA2 in Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1106 b:36.8 occ:1.00 O B:HOH1203 3.1 63.6 1.0 O B:GLN586 3.2 65.2 1.0 O D:GLN586 3.3 66.3 1.0 O C:GLN586 3.4 71.2 1.0 O A:GLN586 3.6 63.3 1.0 O C:GLN587 3.8 90.6 1.0 C B:GLN586 3.9 65.2 1.0 O A:GLN587 4.1 77.0 1.0 C C:GLN586 4.2 71.2 1.0 C D:GLN586 4.2 66.3 1.0 CA C:GLN587 4.3 90.6 1.0 C C:GLN587 4.4 90.6 1.0 C A:GLN586 4.4 63.3 1.0 N B:GLN587 4.5 74.7 1.0 CA B:GLN587 4.5 74.7 1.0 CA D:GLN587 4.6 77.2 1.0 C A:GLN587 4.6 77.0 1.0 N C:GLN587 4.6 90.6 1.0 CA A:GLN587 4.7 77.0 1.0 CB B:GLN586 4.7 65.2 1.0 C B:GLN587 4.7 74.7 1.0 N D:GLN587 4.7 77.2 1.0 CA B:GLN586 4.8 65.2 1.0 O B:GLN587 4.8 74.7 1.0 C D:GLN587 4.9 77.2 1.0 N A:GLN587 4.9 77.0 1.0

S.P.Gangwar, L.Y.Yen, M.V.Yelshanskaya, A.I.Sobolevsky. Modulation of GLUA2-GAMMA5 Synaptic Complex Desensitization, Polyamine Block and Antiepileptic Perampanel Inhibition By Auxiliary Subunit Cornichon-2 Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-01080-X