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

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

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digitoxin, PDB code: 7ddi 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)	16.00 / 3.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.27, 117.715, 491.243, 90, 90, 90
R / Rfree (%)	18.6 / 23.3

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 7ddi). 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: 7ddi:
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:104.2 occ:1.00 OD2 A:ASP740 2.4 125.8 1.0 OD1 A:ASP740 2.8 119.7 1.0 CG A:ASP740 3.0 129.0 1.0 O A:LYS719 3.5 157.1 1.0 O A:GLY272 3.7 176.9 1.0 O A:ALA721 3.8 180.1 1.0 CA A:GLY272 4.0 176.3 1.0 C A:GLY272 4.3 175.4 1.0 CB A:ASP740 4.5 144.4 1.0 C A:LYS719 4.5 159.9 1.0 O A:ASP722 4.6 155.8 1.0 O A:SER718 4.6 169.5 1.0 CA A:LYS719 4.9 164.0 1.0 O A:ALA738 4.9 150.4 1.0 CD A:LYS719 4.9 168.9 1.0 C A:ASP722 4.9 162.7 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:69.9 occ:1.00 OD2 C:ASP740 2.4 123.9 1.0 OD1 C:ASP740 3.1 99.1 1.0 CG C:ASP740 3.1 121.0 1.0 O C:LYS719 3.3 200.8 1.0 O C:GLY272 3.6 146.1 1.0 O C:ALA721 3.8 198.2 1.0 CA C:GLY272 4.2 155.2 1.0 C C:LYS719 4.3 178.6 1.0 C C:GLY272 4.3 159.1 1.0 O C:SER718 4.4 166.5 1.0 CB C:ASP740 4.6 134.3 1.0 CA C:LYS719 4.6 175.0 1.0 CD C:LYS719 4.7 159.2 1.0 O C:ASP722 4.7 155.6 1.0 O C:ALA738 4.8 121.8 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