Sodium in PDB 2auu: Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride

All present enzymatic activity of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride:
3.6.1.1;

The structure of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride, PDB code: 2auu was solved by V.R.Samygina, A.N.Popov, S.M.Avaeva, H.D.Bartunik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.22
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	109.363, 109.363, 75.165, 90.00, 90.00, 120.00
R / Rfree (%)	15 / 18.4

The structure of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride (pdb code 2auu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride, PDB code: 2auu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:32.1 occ:0.75 O A:HOH389 1.2 29.0 0.2 O A:GLU145 2.3 40.2 1.0 O A:HOH337 2.3 42.0 1.0 O A:LYS148 2.4 39.8 1.0 O A:LYS142 2.5 29.0 1.0 O A:HOH390 2.6 30.0 0.3 O A:HOH404 2.7 48.7 1.0 C A:GLU145 3.2 33.7 1.0 C A:LYS148 3.6 46.1 1.0 C A:LYS142 3.6 26.3 1.0 N A:GLU145 3.9 30.9 1.0 NZ A:LYS146 3.9 29.4 0.2 O A:HOH455 4.0 42.0 0.5 N A:LYS148 4.0 48.6 1.0 CA A:GLU145 4.1 33.9 1.0 N A:LYS146 4.1 41.1 1.0 O A:ASP143 4.1 33.4 1.0 C A:ASP143 4.1 29.9 1.0 CA A:LYS148 4.3 43.2 1.0 CA A:LYS146 4.3 46.9 1.0 CA A:ASP143 4.3 27.7 1.0 N A:ASP143 4.4 25.7 1.0 CB A:LYS142 4.4 26.8 1.0 CB A:LYS148 4.5 40.7 1.0 N A:GLY147 4.5 53.5 1.0 N A:TRP149 4.6 44.5 1.0 CD A:LYS146 4.6 42.2 0.2 CA A:TRP149 4.6 47.9 1.0 CA A:LYS142 4.6 25.6 1.0 N A:LEU144 4.6 28.3 1.0 C A:LYS146 4.7 49.7 1.0 CB A:GLU145 4.8 35.8 1.0 C A:LEU144 4.8 33.5 1.0 O A:HOH370 4.8 39.2 1.0 CB A:TRP149 4.8 52.9 1.0 CE A:LYS146 4.9 35.6 0.2

Sodium binding site 2 out of 2 in the Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:16.3 occ:0.85 O A:HOH359 2.4 23.4 0.5 O A:HOH301 2.5 32.8 0.5 O A:HOH347 2.6 25.9 0.5 OD1 A:ASP26 4.1 19.3 1.0 O A:HOH321 4.4 22.8 1.0 O A:HOH481 4.5 38.1 0.5 O A:HOH325 4.5 29.2 1.0 O A:HOH310 4.9 20.7 1.0

V.R.Samygina, V.M.Moiseev, E.V.Rodina, N.N.Vorobyeva, A.N.Popov, S.A.Kurilova, T.I.Nazarova, S.M.Avaeva, H.D.Bartunik. Reversible Inhibition of Escherichia Coli Inorganic Pyrophosphatase By Fluoride: Trapped Catalytic Intermediates in Cryo-Crystallographic Studies J.Mol.Biol. V. 366 1305 2007.
ISSN: ISSN 0022-2836
PubMed: 17196979
DOI: 10.1016/J.JMB.2006.11.082