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

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

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin, PDB code: 7ddk 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 / 3.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	114.357, 118.176, 494.668, 90, 90, 90
R / Rfree (%)	22 / 26.9

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


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 Rostafuroxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:37.2 occ:1.00 OD2 A:ASP740 2.5 76.1 1.0 OD1 A:ASP740 2.8 81.6 1.0 CG A:ASP740 3.1 77.8 1.0 O A:LYS719 3.3 66.7 1.0 CA A:GLY272 3.9 108.0 1.0 O A:GLY272 4.1 71.6 1.0 O A:ALA721 4.2 73.3 1.0 C A:LYS719 4.3 60.4 1.0 O A:SER718 4.4 57.5 1.0 O A:ALA738 4.5 59.1 1.0 C A:GLY272 4.5 99.5 1.0 CD A:LYS719 4.5 92.8 1.0 CA A:LYS719 4.5 65.0 1.0 CB A:ASP740 4.6 74.7 1.0

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


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 Rostafuroxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1102 b:13.4 occ:1.00 OD2 C:ASP740 2.5 55.6 1.0 OD1 C:ASP740 3.0 54.6 1.0 CG C:ASP740 3.1 53.2 1.0 O C:LYS719 3.5 103.0 1.0 O C:GLY272 3.7 79.2 1.0 O C:ALA721 3.9 94.8 1.0 CA C:GLY272 4.1 106.7 1.0 C C:GLY272 4.3 97.8 1.0 C C:LYS719 4.5 103.3 1.0 O C:SER718 4.6 82.4 1.0 CB C:ASP740 4.6 44.9 1.0 O C:ASP722 4.6 54.6 1.0 O C:ALA738 4.8 89.3 1.0 CA C:LYS719 4.9 96.8 1.0 CD C:LYS719 5.0 110.8 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