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

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

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain, PDB code: 7wyt 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 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.621, 117.81, 493.203, 90, 90, 90
R / Rfree (%)	27 / 30.7

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain 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 Ouabain (pdb code 7wyt). 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 Ouabain, PDB code: 7wyt:
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 Ouabain


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 Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:12.8 occ:1.00 OD2 A:ASP740 2.6 30.2 1.0 O A:LYS719 3.3 39.9 1.0 CG A:ASP740 3.3 27.2 1.0 OD1 A:ASP740 3.3 29.4 1.0 O A:GLY272 3.3 69.8 1.0 O A:ALA721 3.7 52.4 1.0 CA A:GLY272 3.8 81.9 1.0 C A:GLY272 4.0 75.9 1.0 C A:LYS719 4.4 32.6 1.0 O A:SER718 4.6 49.2 1.0 O A:ASP722 4.7 22.5 1.0 CB A:ASP740 4.7 21.8 1.0 CA A:LYS719 4.8 33.8 1.0 C A:ALA721 4.9 42.5 1.0

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


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 Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1102 b:9.5 occ:1.00 OD2 C:ASP740 2.4 16.9 1.0 OD1 C:ASP740 2.9 16.9 1.0 CG C:ASP740 3.1 18.0 1.0 O C:LYS719 3.3 27.1 1.0 O C:GLY272 3.7 67.3 1.0 O C:ALA721 3.8 72.7 1.0 CA C:GLY272 4.4 57.8 1.0 C C:LYS719 4.4 27.1 1.0 C C:GLY272 4.5 69.9 1.0 O C:SER718 4.5 45.7 1.0 CB C:ASP740 4.6 20.4 1.0 O C:ASP722 4.7 24.8 1.0 CA C:LYS719 4.8 33.6 1.0

R.Kanai, F.Cornelius, B.Vilsen, C.Toyoshima. Cryoelectron Microscopy of Na + ,K + -Atpase in the Two E2P States with and Without Cardiotonic Steroids. Proc.Natl.Acad.Sci.Usa V. 119 26119 2022.
ISSN: ESSN 1091-6490
PubMed: 35380894
DOI: 10.1073/PNAS.2123226119