Sodium in PDB 8tr5: Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State

The structure of Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State (pdb code 8tr5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State, PDB code: 8tr5:

Sodium binding site 1 out of 1 in the Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na712 b:50.2 occ:1.00 HG C:SER342 2.1 46.7 1.0 HG A:SER342 2.1 46.7 1.0 HG B:SER342 2.2 46.7 1.0 O B:HOH801 2.3 48.8 1.0 O A:HOH801 2.3 48.3 1.0 O C:HOH801 2.3 49.1 1.0 OG C:SER342 2.3 46.7 1.0 OG A:SER342 2.4 46.7 1.0 OG B:SER342 2.4 46.7 1.0 HB2 C:SER342 3.3 46.7 1.0 HB2 A:SER342 3.3 46.7 1.0 HB2 B:SER342 3.4 46.7 1.0 CB C:SER342 3.4 46.7 1.0 CB A:SER342 3.4 46.7 1.0 CB B:SER342 3.4 46.7 1.0 O B:GLY338 3.5 46.0 1.0 H B:SER342 3.5 46.7 1.0 H C:SER342 3.6 46.7 1.0 H A:SER342 3.6 46.7 1.0 O A:GLY338 3.6 46.0 1.0 O C:GLY338 3.6 46.0 1.0 HB3 C:SER342 4.0 46.7 1.0 HB3 A:SER342 4.1 46.7 1.0 N B:SER342 4.1 46.7 1.0 HB3 B:SER342 4.1 46.7 1.0 N C:SER342 4.1 46.7 1.0 N A:SER342 4.2 46.7 1.0 CA C:SER342 4.3 46.7 1.0 CA B:SER342 4.3 46.7 1.0 HB2 B:LEU341 4.3 47.2 1.0 CA A:SER342 4.3 46.7 1.0 HB2 A:LEU341 4.5 47.2 1.0 HB2 C:LEU341 4.5 47.2 1.0 HA B:SER342 4.5 46.7 1.0 HA C:SER342 4.5 46.7 1.0 HA A:SER342 4.6 46.7 1.0 HA B:SER339 4.7 47.6 1.0 HA A:SER339 4.7 47.6 1.0 HA C:SER339 4.7 47.6 1.0 C B:GLY338 4.7 46.0 1.0 O C:HOH836 4.7 30.0 1.0 O C:SER339 4.7 47.6 1.0 O B:SER339 4.7 47.6 1.0 O A:SER339 4.8 47.6 1.0 C A:GLY338 4.8 46.0 1.0 O B:HOH833 4.8 30.0 1.0 O A:HOH834 4.8 30.0 1.0 C C:GLY338 4.8 46.0 1.0 H B:LEU341 5.0 47.2 1.0

A.C.Oken, N.E.Lisi, I.Krishnamurthy, A.E.Mccarthy, M.H.Godsey, A.Glasfeld, S.E.Mansoor. High-Affinity Agonism at the P2X7 Receptor Is Mediated By Three Residues Outside the Orthosteric Pocket Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-50771-6