Sodium in PDB 8ss8: Structure of Ampa Receptor GLUA2 Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State)

The structure of Structure of Ampa Receptor GLUA2 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 Ampa Receptor GLUA2 Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State) (pdb code 8ss8). 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 Ampa Receptor GLUA2 Complex with Auxiliary Subunit Tarp Gamma-5 Bound to Competitive Antagonist Zk and Antiepileptic Drug Perampanel (Closed State), PDB code: 8ss8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Ampa Receptor GLUA2 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 Ampa Receptor GLUA2 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:Na1107 b:28.6 occ:1.00 OG1 C:THR625 3.2 15.8 1.0 OG1 A:THR625 3.5 25.4 1.0 OG1 D:THR625 3.8 18.1 1.0 OG1 B:THR625 3.8 14.8 1.0 O C:ALA621 4.0 37.3 1.0 CB C:THR625 4.1 15.8 1.0 O A:ALA621 4.2 31.6 1.0 CG2 C:THR625 4.2 15.8 1.0 CB C:ALA621 4.3 37.3 1.0 O B:ALA621 4.3 11.0 1.0 CB A:THR625 4.3 25.4 1.0 CB D:ALA621 4.3 14.9 1.0 CB B:ALA621 4.3 11.0 1.0 O D:ALA621 4.4 14.9 1.0 CB A:ALA621 4.4 31.6 1.0 CG2 A:THR625 4.4 25.4 1.0 C C:ALA621 4.4 37.3 1.0 C A:ALA621 4.6 31.6 1.0 C B:ALA621 4.7 11.0 1.0 C D:ALA621 4.8 14.9 1.0 CB B:THR625 4.8 14.8 1.0 CB D:THR625 4.8 18.1 1.0 CG2 D:THR625 4.8 18.1 1.0 CG2 B:THR625 4.8 14.8 1.0 CA C:ALA621 4.9 37.3 1.0 N C:ALA622 5.0 41.4 1.0

Sodium binding site 2 out of 2 in the Structure of Ampa Receptor GLUA2 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 Ampa Receptor GLUA2 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:28.6 occ:1.00 O C:GLN586 2.9 85.2 1.0 O A:GLN586 3.1 84.6 1.0 O B:GLN586 3.4 83.2 1.0 O D:GLN586 3.5 88.9 1.0 C C:GLN586 4.1 85.2 1.0 C A:GLN586 4.2 84.6 1.0 C B:GLN586 4.3 83.2 1.0 C D:GLN586 4.5 88.9 1.0 N B:GLY588 4.7 105.7 1.0 CB A:GLN586 4.8 84.6 1.0 CB B:GLN586 4.8 83.2 1.0 N D:GLY588 4.8 112.3 1.0 CA C:GLN587 4.8 100.5 1.0 CB C:GLN586 4.8 85.2 1.0 N C:GLN587 4.8 100.5 1.0 N C:GLY588 4.9 118.7 1.0 C C:GLN587 4.9 100.5 1.0 N A:GLY588 4.9 116.2 1.0 N B:GLN587 5.0 94.5 1.0 N A:GLN587 5.0 100.2 1.0 CA C:GLN586 5.0 85.2 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