Sodium in PDB 8ijm: Cyo-Em Structure of K794A Non-Gastric Proton Pump in Na+ Bound E1AMPPCP State

The binding sites of Sodium atom in the Cyo-Em Structure of K794A Non-Gastric Proton Pump in Na+ Bound E1AMPPCP State (pdb code 8ijm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cyo-Em Structure of K794A Non-Gastric Proton Pump in Na+ Bound E1AMPPCP State, PDB code: 8ijm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cyo-Em Structure of K794A Non-Gastric Proton Pump in Na+ Bound E1AMPPCP State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cyo-Em Structure of K794A Non-Gastric Proton Pump in Na+ Bound E1AMPPCP State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1105 b:33.6 occ:1.00 OD1 A:ASN795 2.3 33.9 1.0 O A:THR791 2.8 36.0 1.0 OD1 A:ASP827 3.3 46.8 1.0 CG A:ASN795 3.3 29.4 1.0 OD1 A:ASP823 3.5 45.4 1.0 O A:ALA794 3.6 37.2 1.0 ND2 A:ASN795 3.8 26.4 1.0 NA A:NA1106 3.8 29.3 1.0 O A:ALA342 3.8 44.4 1.0 C A:THR791 3.8 29.4 1.0 CG2 A:THR791 4.0 24.9 1.0 C A:ALA794 4.3 35.0 1.0 CG A:ASP823 4.4 47.6 1.0 CG A:ASP827 4.4 46.4 1.0 CA A:THR791 4.5 27.0 1.0 CB A:ASN795 4.6 24.9 1.0 CA A:ASN795 4.8 26.6 1.0 N A:LEU792 4.8 23.2 1.0 OD2 A:ASP823 4.8 46.5 1.0 N A:ASN795 4.8 37.2 1.0 CB A:THR791 4.9 24.3 1.0 CA A:LEU792 5.0 15.6 1.0

Sodium binding site 2 out of 2 in the Cyo-Em Structure of K794A Non-Gastric Proton Pump in Na+ Bound E1AMPPCP State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cyo-Em Structure of K794A Non-Gastric Proton Pump in Na+ Bound E1AMPPCP State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1106 b:29.3 occ:1.00 OE1 A:GLN942 2.7 16.4 1.0 CB A:ALA794 3.0 25.4 1.0 O A:THR791 3.3 36.0 1.0 OD1 A:ASP827 3.3 46.8 1.0 CD A:GLN942 3.4 20.2 1.0 O A:TYR790 3.4 31.8 1.0 NE2 A:GLN942 3.5 22.7 1.0 N A:ALA794 3.7 30.5 1.0 CA A:ALA794 3.8 24.7 1.0 NA A:NA1105 3.8 33.6 1.0 O A:ALA794 3.9 37.2 1.0 C A:THR791 4.0 29.4 1.0 CA A:THR791 4.1 27.0 1.0 C A:ALA794 4.2 35.0 1.0 CG A:ASP827 4.2 46.4 1.0 CB A:ASP827 4.3 44.1 1.0 C A:TYR790 4.5 22.9 1.0 N A:THR791 4.8 25.2 1.0 CG A:GLN942 4.8 13.2 1.0 CE1 A:TYR790 4.9 22.9 1.0 C A:THR793 5.0 20.8 1.0 OE2 A:GLU798 5.0 35.2 1.0 O A:THR826 5.0 44.0 1.0 CA A:ASP827 5.0 42.9 1.0

K.Abe, P.Nishizawa, P.Artigas. An Unusual Conformation From Na+-Sensitive Non-Gastric Proton Pump Mutants Reveals Molecular Mechanisms of Cooperative Na+-Binding. Biochim.Biophys.Acta 2023.
ISSN: ISSN 0006-3002
DOI: 10.1016/J.BBAMCR.2023.119543