Sodium in PDB 6k21: Pyrophosphatase From Acinetobacter Baumannii

All present enzymatic activity of Pyrophosphatase From Acinetobacter Baumannii:
3.6.1.1;

The structure of Pyrophosphatase From Acinetobacter Baumannii, PDB code: 6k21 was solved by J.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 2.00
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.813, 102.813, 100.776, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 21.3

The structure of Pyrophosphatase From Acinetobacter Baumannii also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Pyrophosphatase From Acinetobacter Baumannii (pdb code 6k21). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Pyrophosphatase From Acinetobacter Baumannii, PDB code: 6k21:

Sodium binding site 1 out of 1 in the Pyrophosphatase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pyrophosphatase From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:51.9 occ:1.00 O A:ASP143 2.7 24.1 1.0 O A:GLU145 3.1 31.5 1.0 O A:LYS148 3.3 41.9 1.0 O A:HOH507 3.5 50.3 1.0 O A:HOH583 3.5 41.3 1.0 C A:ASP143 3.5 22.1 1.0 C A:GLU145 3.9 32.3 1.0 O A:LYS142 4.0 22.6 1.0 N A:LYS148 4.1 43.1 1.0 CA A:ASP143 4.2 21.6 1.0 N A:GLY147 4.2 38.3 1.0 CA A:PRO146 4.3 38.2 1.0 N A:GLU145 4.3 26.6 1.0 C A:LYS148 4.3 41.5 1.0 N A:LEU144 4.4 20.1 1.0 N A:PRO146 4.5 41.6 1.0 C A:PRO146 4.6 36.4 1.0 CA A:LEU144 4.6 24.5 1.0 C A:LEU144 4.6 28.5 1.0 CA A:LYS148 4.7 39.4 1.0 CA A:GLU145 4.8 31.7 1.0 C A:LYS142 5.0 20.1 1.0

Y.Si, X.Wang, G.Yang, T.Yang, Y.Li, G.J.Ayala, X.Li, H.Wang, J.Su. Crystal Structures of Pyrophosphatase From Acinetobacter Baumannii: Snapshots of Pyrophosphate Binding and Identification of A Phosphorylated Enzyme Intermediate. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 31500178
DOI: 10.3390/IJMS20184394