Sodium in PDB 7ddh: Crystal Structures of Na+,K+-Atpase in Complex with Digoxin

All present enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin:
7.2.2.13;

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin, PDB code: 7ddh was solved by H.Ogawa, F.Cornelius, R.Kanai, K.Motoyama, B.Vilsen, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.99 / 3.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	114.973, 118.493, 495.137, 90, 90, 90
R / Rfree (%)	24.1 / 27.2

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Crystal Structures of Na+,K+-Atpase in Complex with Digoxin (pdb code 7ddh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structures of Na+,K+-Atpase in Complex with Digoxin, PDB code: 7ddh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structures of Na+,K+-Atpase in Complex with Digoxin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:50.7 occ:1.00 OD2 A:ASP740 2.4 91.5 1.0 OD1 A:ASP740 2.8 88.7 1.0 CG A:ASP740 2.9 97.5 1.0 O A:LYS719 3.5 72.9 1.0 O A:GLY272 3.9 94.0 1.0 CA A:GLY272 4.1 119.4 1.0 O A:ALA721 4.2 83.6 1.0 C A:GLY272 4.5 117.8 1.0 CB A:ASP740 4.5 104.3 1.0 C A:LYS719 4.5 72.9 1.0 O A:SER718 4.6 119.3 1.0 CA A:LYS719 4.8 72.9 1.0 CD A:LYS719 4.8 93.5 1.0 O A:ASP722 4.9 79.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structures of Na+,K+-Atpase in Complex with Digoxin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1102 b:41.6 occ:1.00 OD2 C:ASP740 2.4 93.1 1.0 OD1 C:ASP740 2.9 78.5 1.0 CG C:ASP740 3.0 87.2 1.0 O C:LYS719 3.4 118.5 1.0 O C:GLY272 3.6 118.9 1.0 O C:ALA721 4.0 90.7 1.0 CA C:GLY272 4.2 117.3 1.0 C C:GLY272 4.3 121.9 1.0 C C:LYS719 4.4 96.8 1.0 O C:SER718 4.5 129.0 1.0 CB C:ASP740 4.5 71.4 1.0 CA C:LYS719 4.7 87.4 1.0 O C:ASP722 4.8 82.2 1.0 CD C:LYS719 4.9 93.9 1.0

R.Kanai, F.Cornelius, H.Ogawa, K.Motoyama, B.Vilsen, C.Toyoshima. Binding of Cardiotonic Steroids to Na + ,K + -Atpase in the E2P State. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33318128
DOI: 10.1073/PNAS.2020438118