Sodium in PDB 8sgi: Cryo-Em Structure of Human NCX1 in Complex with SEA0400

The structure of Cryo-Em Structure of Human NCX1 in Complex with SEA0400 also contains other interesting chemical elements:

Calcium	(Ca)	6 atoms
Fluorine	(F)	2 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of Human NCX1 in Complex with SEA0400 (pdb code 8sgi). 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 Complex with SEA0400, PDB code: 8sgi:
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 Complex with SEA0400


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 Complex with SEA0400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1008 b:30.0 occ:1.00 O A:SER109 2.2 22.2 1.0 O A:THR810 2.3 20.6 1.0 OE1 A:GLU113 2.4 19.9 1.0 OE2 A:GLU113 2.7 19.9 1.0 OD1 A:ASP814 2.7 23.7 1.0 CD A:GLU113 2.9 19.9 1.0 C A:SER109 3.3 22.2 1.0 C A:THR810 3.4 20.6 1.0 O A:HOH1101 3.7 21.8 1.0 CG A:ASP814 3.7 23.7 1.0 CA A:SER110 3.7 21.1 1.0 N A:SER110 3.9 21.1 1.0 CD A:PRO112 3.9 19.7 1.0 OD2 A:ASP814 4.0 23.7 1.0 CG A:PRO112 4.1 19.7 1.0 CA A:SER811 4.1 21.0 1.0 N A:SER811 4.2 21.0 1.0 CB A:PRO112 4.3 19.7 1.0 C A:SER110 4.4 21.1 1.0 CG A:GLU113 4.4 19.9 1.0 CB A:THR810 4.4 20.6 1.0 CA A:THR810 4.4 20.6 1.0 CA A:SER109 4.5 22.2 1.0 CG A:PRO813 4.6 22.4 1.0 CB A:PRO813 4.6 22.4 1.0 N A:PRO112 4.6 19.7 1.0 N A:GLU113 4.7 19.9 1.0 CB A:SER109 4.7 22.2 1.0 CD A:PRO813 4.7 22.4 1.0 NA A:NA1009 4.8 27.4 1.0 OG1 A:THR810 4.8 20.6 1.0 N A:ALA111 4.8 19.7 1.0 CB A:SER110 4.9 21.1 1.0 N A:ASP814 4.9 23.7 1.0 O A:SER110 5.0 21.1 1.0 C A:SER811 5.0 21.0 1.0 OG A:SER811 5.0 21.0 1.0

Sodium binding site 2 out of 3 in the Cryo-Em Structure of Human NCX1 in Complex with SEA0400


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 Complex with SEA0400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1009 b:27.4 occ:1.00 OG A:SER811 2.4 21.0 1.0 OG A:SER139 2.4 20.3 1.0 OG1 A:THR810 2.4 20.6 1.0 O A:ALA807 2.7 20.6 1.0 OE2 A:GLU113 2.9 19.9 1.0 CB A:SER139 3.1 20.3 1.0 N A:SER811 3.3 21.0 1.0 CD A:GLU113 3.4 19.9 1.0 CG A:GLU113 3.5 19.9 1.0 CB A:SER811 3.5 21.0 1.0 C A:THR810 3.5 20.6 1.0 CB A:THR810 3.6 20.6 1.0 C A:ALA807 3.6 20.6 1.0 CA A:SER811 3.8 21.0 1.0 CA A:ALA807 3.8 20.6 1.0 CA A:SER139 3.9 20.3 1.0 CA A:THR810 4.0 20.6 1.0 O A:THR810 4.0 20.6 1.0 N A:THR810 4.3 20.6 1.0 OE1 A:GLU113 4.3 19.9 1.0 O A:THR135 4.4 21.4 1.0 O A:VAL806 4.4 23.8 1.0 O A:HOH1101 4.4 21.8 1.0 CB A:ALA807 4.6 20.6 1.0 NA A:NA1008 4.8 30.0 1.0 CG2 A:THR810 4.8 20.6 1.0 N A:LEU808 4.9 22.3 1.0 OG1 A:THR135 4.9 21.4 1.0 N A:SER139 4.9 20.3 1.0 N A:ALA807 5.0 20.6 1.0 CB A:GLU113 5.0 19.9 1.0

Sodium binding site 3 out of 3 in the Cryo-Em Structure of Human NCX1 in Complex with SEA0400


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 Complex with SEA0400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1010 b:27.6 occ:1.00 O A:ALA106 2.4 22.7 1.0 OD2 A:ASP814 2.4 23.7 1.0 OG A:SER838 2.4 21.6 1.0 OG A:SER109 2.4 22.2 1.0 OG A:SER110 2.4 21.1 1.0 CB A:SER838 3.2 21.6 1.0 C A:ALA106 3.3 22.7 1.0 N A:SER110 3.3 21.1 1.0 CB A:SER109 3.5 22.2 1.0 CA A:ALA106 3.5 22.7 1.0 CG A:ASP814 3.6 23.7 1.0 C A:SER109 3.6 22.2 1.0 CB A:SER110 3.6 21.1 1.0 CA A:SER838 3.8 21.6 1.0 CA A:SER110 3.9 21.1 1.0 CA A:SER109 3.9 22.2 1.0 O A:HOH1101 4.1 21.8 1.0 CB A:ALA106 4.1 22.7 1.0 N A:SER109 4.2 22.2 1.0 O A:SER109 4.2 22.2 1.0 OD1 A:ASP814 4.3 23.7 1.0 ND2 A:ASN834 4.4 27.5 1.0 CB A:ASP814 4.5 23.7 1.0 N A:LEU107 4.5 22.9 1.0 O A:MET105 4.5 25.0 1.0 N A:SER838 4.6 21.6 1.0 O A:ASN834 4.8 27.5 1.0 N A:ALA106 4.8 22.7 1.0 C A:SER838 5.0 21.6 1.0

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