Sodium in PDB 8sgj: Cryo-Em Structure of Human NCX1 in Apo Inactivated State

The structure of Cryo-Em Structure of Human NCX1 in Apo Inactivated State also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of Human NCX1 in Apo Inactivated State (pdb code 8sgj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cryo-Em Structure of Human NCX1 in Apo Inactivated State, PDB code: 8sgj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cryo-Em Structure of Human NCX1 in Apo Inactivated 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 Human NCX1 in Apo Inactivated State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1007 b:30.0 occ:1.00 O A:THR810 2.3 41.9 1.0 O A:SER109 2.4 42.0 1.0 OD1 A:ASP814 2.6 45.2 1.0 OE2 A:GLU113 2.7 39.2 1.0 OE1 A:GLU113 3.2 39.2 1.0 CD A:GLU113 3.3 39.2 1.0 O A:HOH1101 3.4 46.5 1.0 C A:THR810 3.5 41.9 1.0 C A:SER109 3.5 42.0 1.0 CG A:ASP814 3.6 45.2 1.0 CA A:SER811 3.9 43.4 1.0 CA A:SER110 3.9 41.4 1.0 OD2 A:ASP814 4.0 45.2 1.0 N A:SER811 4.1 43.4 1.0 N A:SER110 4.2 41.4 1.0 CD A:PRO112 4.3 39.4 1.0 CG A:PRO112 4.6 39.4 1.0 CA A:THR810 4.6 41.9 1.0 CB A:THR810 4.6 41.9 1.0 C A:SER110 4.6 41.4 1.0 CA A:SER109 4.7 42.0 1.0 C A:SER811 4.7 43.4 1.0 NA A:NA1009 4.7 46.2 1.0 OG A:SER811 4.8 43.4 1.0 CG A:GLU113 4.8 39.2 1.0 CB A:PRO112 4.8 39.4 1.0 OG1 A:THR810 4.9 41.9 1.0 CB A:SER811 4.9 43.4 1.0 CD A:PRO813 4.9 43.6 1.0 CB A:SER109 4.9 42.0 1.0 CB A:ASP814 4.9 45.2 1.0 N A:ASP814 4.9 45.2 1.0 CB A:SER110 5.0 41.4 1.0

Sodium binding site 2 out of 3 in the Cryo-Em Structure of Human NCX1 in Apo Inactivated State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of Human NCX1 in Apo Inactivated State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1008 b:49.5 occ:1.00 OG A:SER139 2.4 43.8 1.0 O A:ALA807 2.4 43.3 1.0 OG A:SER811 2.4 43.4 1.0 OE1 A:GLU113 2.4 39.2 1.0 OG1 A:THR810 2.5 41.9 1.0 C A:ALA807 3.2 43.3 1.0 CB A:SER139 3.2 43.8 1.0 CA A:ALA807 3.2 43.3 1.0 N A:SER811 3.3 43.4 1.0 CB A:SER811 3.5 43.4 1.0 CD A:GLU113 3.6 39.2 1.0 C A:THR810 3.6 41.9 1.0 CB A:THR810 3.7 41.9 1.0 CA A:SER139 3.7 43.8 1.0 CA A:SER811 3.8 43.4 1.0 CA A:THR810 4.0 41.9 1.0 CB A:ALA807 4.0 43.3 1.0 CG A:GLU113 4.0 39.2 1.0 O A:VAL806 4.0 46.0 1.0 N A:THR810 4.1 41.9 1.0 O A:THR810 4.1 41.9 1.0 N A:ALA807 4.4 43.3 1.0 N A:LEU808 4.5 43.4 1.0 O A:THR135 4.5 44.8 1.0 N A:SER139 4.5 43.8 1.0 OE2 A:GLU113 4.6 39.2 1.0 C A:VAL806 4.7 46.0 1.0 OG1 A:THR135 4.7 44.8 1.0 CG2 A:THR810 4.8 41.9 1.0 O A:HOH1101 4.9 46.5 1.0 C A:SER139 4.9 43.8 1.0

Sodium binding site 3 out of 3 in the Cryo-Em Structure of Human NCX1 in Apo Inactivated State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of Human NCX1 in Apo Inactivated State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1009 b:46.2 occ:1.00 OD2 A:ASP814 2.4 45.2 1.0 OG A:SER109 2.4 42.0 1.0 OG A:SER110 2.4 41.4 1.0 O A:ALA106 2.4 40.8 1.0 OG A:SER838 2.4 41.3 1.0 N A:SER110 3.0 41.4 1.0 C A:SER109 3.1 42.0 1.0 CB A:SER838 3.2 41.3 1.0 CB A:SER109 3.2 42.0 1.0 C A:ALA106 3.4 40.8 1.0 CG A:ASP814 3.5 45.2 1.0 CB A:SER110 3.5 41.4 1.0 O A:SER109 3.6 42.0 1.0 CA A:SER110 3.6 41.4 1.0 CA A:SER109 3.6 42.0 1.0 CA A:ALA106 3.7 40.8 1.0 CA A:SER838 3.9 41.3 1.0 OD1 A:ASP814 4.0 45.2 1.0 N A:SER109 4.0 42.0 1.0 O A:HOH1101 4.0 46.5 1.0 CB A:ALA106 4.2 40.8 1.0 ND2 A:ASN834 4.5 45.6 1.0 CB A:ASP814 4.6 45.2 1.0 N A:LEU107 4.6 40.9 1.0 NA A:NA1007 4.7 30.0 1.0 O A:MET105 4.7 43.1 1.0 N A:SER838 4.8 41.3 1.0 O A:ASN834 4.9 45.6 1.0 N A:ALA106 5.0 40.8 1.0

J.Xue, Y.Han, W.Zeng, Y.Jiang. Structural Mechanisms of Human Cardiac Sodium Calcium Exchanger NCX1 To Be Published.