Sodium in PDB 6kpx: Crystal Structures of Na+,K+-Atpase in Complex with Digitoxin

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digitoxin, PDB code: 6kpx was solved by H.Ogawa, K.Motoyama, F.Cornelius, B.Vilsen, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.00 / 3.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.270, 117.715, 491.243, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.7

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digitoxin 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 Digitoxin (pdb code 6kpx). 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 Digitoxin, PDB code: 6kpx:
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 Digitoxin


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 Digitoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:0.8 occ:1.00 OD2 A:ASP740 2.6 0.4 1.0 OD1 A:ASP740 3.0 0.5 1.0 CG A:ASP740 3.2 0.4 1.0 O A:LYS719 3.2 0.3 1.0 O A:GLY272 3.7 0.6 1.0 O A:ALA721 3.8 0.6 1.0 CA A:GLY272 3.8 0.9 1.0 C A:GLY272 4.2 0.9 1.0 C A:LYS719 4.3 0.6 1.0 O A:LEU718 4.6 0.7 1.0 CA A:LYS719 4.7 0.3 1.0 CB A:ASP740 4.7 0.0 1.0 CD A:LYS719 4.8 0.6 1.0 O A:ALA738 4.9 0.2 1.0 O A:ASP722 4.9 0.7 1.0 C A:ALA721 5.0 0.8 1.0

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


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 Digitoxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1102 b:68.0 occ:1.00 OD2 C:ASP740 2.6 0.2 1.0 OD1 C:ASP740 2.9 88.9 1.0 CG C:ASP740 3.1 1.0 1.0 O C:LYS719 3.3 0.1 1.0 O C:GLY272 3.6 0.5 1.0 O C:ALA721 3.8 0.5 1.0 CA C:GLY272 4.2 0.4 1.0 C C:LYS719 4.3 0.0 1.0 C C:GLY272 4.3 0.2 1.0 O C:LEU718 4.4 1.0 1.0 CB C:ASP740 4.6 0.8 1.0 CA C:LYS719 4.6 0.1 1.0 CD C:LYS719 4.7 0.1 1.0 O C:ALA738 4.8 0.2 1.0 O C:ASP722 4.9 0.3 1.0

H.Ogawa, K.Motoyama, F.Cornelius, B.Vilsen, C.Toyoshima. X-Ray Crystal Structures of Na+,K+-Atpase in Complex with Cardiotonic Steroids To Be Published.