Sodium in PDB 8ijl: Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp

The structure of Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Aluminium	(Al)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp (pdb code 8ijl). 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 Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp, PDB code: 8ijl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp


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 Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1110 b:19.6 occ:1.00 O A:VAL344 2.6 44.8 1.0 O A:ALA342 2.8 43.7 1.0 OD2 A:ASP823 2.9 53.9 1.0 OE1 A:GLU798 3.0 39.0 1.0 O A:VAL341 3.1 46.7 1.0 OD1 A:ASP823 3.1 46.5 1.0 OD1 A:ASN795 3.1 34.7 1.0 CG A:ASP823 3.4 49.7 1.0 C A:ALA342 3.4 36.4 1.0 OE1 A:GLU346 3.5 46.5 1.0 C A:VAL344 3.6 40.2 1.0 CA A:ALA342 3.8 34.5 1.0 CG A:ASN795 3.9 37.8 1.0 CD A:GLU798 4.0 36.9 1.0 N A:VAL344 4.1 35.3 1.0 C A:VAL341 4.1 37.0 1.0 N A:PRO345 4.3 38.2 1.0 N A:ASN343 4.3 45.7 1.0 CA A:PRO345 4.4 39.1 1.0 OE2 A:GLU798 4.4 36.3 1.0 ND2 A:ASN795 4.4 31.0 1.0 C A:ASN343 4.5 41.1 1.0 CA A:VAL344 4.5 37.7 1.0 N A:ALA342 4.5 36.0 1.0 CD A:GLU346 4.5 43.5 1.0 CE A:LYS794 4.5 34.2 1.0 OE2 A:GLU346 4.8 44.5 1.0 CB A:ASN795 4.8 31.0 1.0 CA A:ASN795 4.8 21.6 1.0 CD A:LYS794 4.8 33.4 1.0 CA A:ASN343 4.8 37.5 1.0 CB A:ASP823 4.9 40.0 1.0 N A:GLU346 4.9 40.2 1.0

Sodium binding site 2 out of 2 in the Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp


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 Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1111 b:41.9 occ:1.00 O A:ALA740 2.7 32.1 1.0 OD2 A:ASP759 2.8 34.3 1.0 O A:LEU737 3.2 38.0 1.0 O A:HOH1203 3.4 35.7 1.0 O A:LYS738 3.4 41.5 1.0 CG A:ASP759 3.6 38.2 1.0 OD1 A:ASP759 3.7 47.9 1.0 C A:ALA740 3.8 29.3 1.0 O A:ASP741 3.9 36.2 1.0 N A:GLY743 3.9 29.4 1.0 C A:LYS738 4.1 29.3 1.0 C A:ASP741 4.1 26.7 1.0 CA A:LYS738 4.3 25.5 1.0 CA A:ILE742 4.3 19.8 1.0 C A:ILE742 4.3 23.0 1.0 C A:LEU737 4.4 34.4 1.0 N A:ILE742 4.4 26.7 1.0 N A:ALA740 4.5 31.8 1.0 CA A:ALA740 4.6 25.4 1.0 CA A:GLY743 4.6 19.2 1.0 O A:ALA757 4.7 40.2 1.0 N A:ASP741 4.7 29.4 1.0 CA A:ASP741 4.8 21.2 1.0 N A:LYS738 4.9 38.6 1.0 CB A:ALA740 4.9 19.9 1.0 C A:LYS739 5.0 33.8 1.0 NZ A:LYS738 5.0 40.8 1.0

K.Abe, T.Nishizawa, P.Artigas. An Unusual Conformation From Na + -Sensitive Non-Gastric Proton Pump Mutants Reveals Molecular Mechanisms of Cooperative Na + -Binding. Biochim Biophys Acta Mol V.1870 19543 2023CELL Res.
ISSN: ISSN 1879-2596
PubMed: 37482134
DOI: 10.1016/J.BBAMCR.2023.119543