Sodium in PDB 7ddf: Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride

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

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride, PDB code: 7ddf 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 / 4.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	114.481, 118.371, 495.388, 90, 90, 90
R / Rfree (%)	19.4 / 24.2

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Magnesium	(Mg)	4 atoms

The binding sites of Sodium atom in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride (pdb code 7ddf). 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 Beryllium Fluoride, PDB code: 7ddf:
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 Beryllium Fluoride


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 Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:33.6 occ:1.00 OD2 A:ASP740 2.5 89.1 1.0 OD1 A:ASP740 3.0 89.2 1.0 CG A:ASP740 3.1 92.3 1.0 O A:LYS719 3.5 130.2 1.0 O A:GLY272 3.6 137.1 1.0 CA A:GLY272 3.6 140.2 1.0 O A:ALA721 3.9 120.9 1.0 C A:GLY272 4.1 139.1 1.0 O A:ASP722 4.4 99.7 1.0 C A:LYS719 4.5 129.7 1.0 CB A:ASP740 4.6 100.3 1.0 CD A:LYS719 4.7 127.0 1.0 O A:SER718 4.8 128.0 1.0 CA A:LYS719 4.9 129.5 1.0 C A:ASP722 4.9 101.8 1.0 N A:GLY272 4.9 143.2 1.0

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


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 Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1102 b:56.9 occ:1.00 OD2 C:ASP740 2.5 98.5 1.0 O C:GLY272 3.1 158.9 1.0 O C:LYS719 3.1 133.3 1.0 OD1 C:ASP740 3.3 98.8 1.0 CG C:ASP740 3.3 100.5 1.0 CA C:GLY272 3.5 164.4 1.0 O C:ALA721 3.5 135.6 1.0 C C:GLY272 3.7 162.2 1.0 C C:LYS719 4.2 133.7 1.0 O C:ASP722 4.3 129.4 1.0 O C:SER718 4.6 131.5 1.0 CA C:LYS719 4.6 133.8 1.0 CD C:LYS719 4.7 130.5 1.0 C C:ASP722 4.7 131.9 1.0 CB C:ASP740 4.8 105.2 1.0 C C:ALA721 4.8 135.1 1.0 N C:GLY272 4.8 171.1 1.0 N C:GLY273 5.0 166.6 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