Sodium in PDB 2au9: Inorganic Pyrophosphatase Complexed with Substrate

All present enzymatic activity of Inorganic Pyrophosphatase Complexed with Substrate:
3.6.1.1;

The structure of Inorganic Pyrophosphatase Complexed with Substrate, PDB code: 2au9 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 / 1.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	110.247, 110.247, 74.612, 90.00, 90.00, 120.00
R / Rfree (%)	14.9 / 18.2

The structure of Inorganic Pyrophosphatase Complexed with Substrate also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Manganese	(Mn)	5 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Inorganic Pyrophosphatase Complexed with Substrate (pdb code 2au9). 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 Substrate, PDB code: 2au9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Inorganic Pyrophosphatase Complexed with Substrate


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 Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:27.5 occ:1.00 O A:LYS148 2.3 30.3 1.0 O A:GLU145 2.3 27.7 1.0 O A:HOH335 2.3 33.4 1.0 O A:LYS142 2.4 22.3 1.0 O A:HOH471 2.5 34.5 1.0 O A:HOH390 2.9 37.8 1.0 C A:GLU145 3.2 26.0 1.0 C A:LYS148 3.4 28.2 1.0 C A:LYS142 3.6 23.7 1.0 N A:GLU145 3.9 24.6 1.0 N A:LYS148 3.9 30.9 1.0 CA A:GLU145 4.1 26.4 1.0 N A:LYS146 4.1 30.9 1.0 CA A:LYS148 4.1 30.7 1.0 CA A:LYS146 4.2 32.4 1.0 C A:ASP143 4.2 23.9 1.0 O A:ASP143 4.3 27.2 1.0 CA A:ASP143 4.3 24.5 1.0 N A:GLY147 4.4 36.7 1.0 CB A:LYS142 4.4 23.4 1.0 CB A:LYS148 4.4 29.1 0.9 O A:HOH362 4.4 30.9 1.0 C A:LYS146 4.4 34.4 1.0 N A:ASP143 4.4 22.5 1.0 N A:TRP149 4.5 29.1 1.0 O A:HOH439 4.6 47.1 1.0 CA A:LYS142 4.6 21.1 1.0 CB A:GLU145 4.6 23.1 0.8 CA A:TRP149 4.7 26.8 1.0 N A:LEU144 4.7 24.8 1.0 O A:HOH485 4.7 40.6 1.0 O A:HOH461 4.8 32.9 0.5 CB A:TRP149 4.9 32.6 1.0 C A:LEU144 4.9 27.9 1.0

Sodium binding site 2 out of 2 in the Inorganic Pyrophosphatase Complexed with Substrate


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 Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:17.9 occ:1.00 O A:HOH472 2.5 18.0 1.0 O A:HOH355 2.5 18.6 0.5 OD1 A:ASP26 4.2 19.4 1.0 MN A:MN205 4.4 31.5 0.5 O A:HOH324 4.5 25.0 1.0 O A:HOH310 4.8 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