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

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

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Bufalin, PDB code: 7ddl 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)	14.99 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.721, 117.646, 492.068, 90, 90, 90
R / Rfree (%)	24.1 / 28.1

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


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 Bufalin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:15.9 occ:1.00 OD2 A:ASP740 2.4 106.1 1.0 CG A:ASP740 3.2 106.6 1.0 OD1 A:ASP740 3.2 106.6 1.0 O A:LYS719 3.3 85.6 1.0 O A:GLY272 3.6 127.2 1.0 O A:ALA721 3.8 77.7 1.0 CA A:GLY272 4.0 142.7 1.0 C A:GLY272 4.3 130.2 1.0 C A:LYS719 4.3 92.6 1.0 O A:SER718 4.4 86.6 1.0 CB A:ASP740 4.6 104.2 1.0 O A:ASP722 4.7 91.6 1.0 CA A:LYS719 4.7 89.2 1.0 CD A:LYS719 5.0 115.2 1.0

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


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 Bufalin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1102 b:15.9 occ:1.00 OD2 C:ASP740 2.4 64.7 1.0 OD1 C:ASP740 3.1 52.0 1.0 CG C:ASP740 3.1 56.1 1.0 O C:LYS719 3.2 97.8 1.0 O C:GLY272 3.7 121.1 1.0 O C:ALA721 3.8 108.9 1.0 CA C:GLY272 4.1 113.3 1.0 C C:LYS719 4.3 113.1 1.0 C C:GLY272 4.4 120.8 1.0 O C:SER718 4.5 110.3 1.0 CB C:ASP740 4.6 48.9 1.0 O C:ASP722 4.7 86.5 1.0 CA C:LYS719 4.7 111.0 1.0 O C:ALA738 5.0 71.3 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