Sodium in PDB 1i40: Structure of Inorganic Pyrophosphatase

All present enzymatic activity of Structure of Inorganic Pyrophosphatase:
3.6.1.1;

The structure of Structure of Inorganic Pyrophosphatase, PDB code: 1i40 was solved by V.R.Samygina, A.N.Popov, V.S.Lamzin, S.M.Avaeva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 1.10
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	109.520, 109.520, 75.080, 90.00, 90.00, 120.00
R / Rfree (%)	11.7 / 15.3

The structure of Structure of Inorganic Pyrophosphatase also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Calcium	(Ca)	5 atoms

The binding sites of Sodium atom in the Structure of Inorganic Pyrophosphatase (pdb code 1i40). 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 Structure of Inorganic Pyrophosphatase, PDB code: 1i40:

Sodium binding site 1 out of 1 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:18.7 occ:1.00 O A:GLU145 2.3 19.6 1.0 O A:LYS148 2.3 22.0 1.0 O A:LYS142 2.4 15.6 1.0 O A:HOH352 2.4 32.5 1.0 O A:HOH413 2.6 30.2 0.6 O A:HOH342 2.7 16.2 1.0 C A:GLU145 3.3 17.4 1.0 C A:LYS148 3.5 19.1 1.0 C A:LYS142 3.6 13.9 1.0 N A:GLU145 3.8 16.5 1.0 O A:LYS146 4.0 27.8 0.4 CA A:GLU145 4.0 17.2 1.0 O A:ASP143 4.1 18.4 1.0 C A:ASP143 4.1 15.7 1.0 N A:LYS148 4.2 22.1 1.0 N A:LYS146 4.3 19.0 0.6 CA A:ASP143 4.3 15.1 1.0 N A:LYS146 4.3 19.2 0.4 C A:LYS146 4.3 22.4 0.4 CB A:LYS142 4.3 14.6 0.3 CA A:TRP149 4.4 21.4 1.0 N A:TRP149 4.4 21.5 1.0 N A:ASP143 4.4 14.9 1.0 CB A:GLU145 4.4 18.2 1.0 CA A:LYS146 4.4 18.8 0.6 CB A:LYS142 4.5 15.4 0.7 CB A:TRP149 4.5 23.6 1.0 CA A:LYS148 4.5 20.7 1.0 CA A:LYS146 4.5 20.5 0.4 O A:HOH408 4.5 51.3 1.0 N A:LEU144 4.5 16.0 1.0 CA A:LYS142 4.6 13.7 1.0 C A:LEU144 4.7 17.7 1.0 N A:GLY147 4.7 18.2 0.6 C A:LYS146 4.8 16.9 0.6 O A:HOH396 4.9 20.7 1.0

V.R.Samygina, A.N.Popov, E.V.Rodina, N.N.Vorobyeva, V.S.Lamzin, K.M.Polyakov, S.A.Kurilova, T.I.Nazarova, S.M.Avaeva. The Structures of Escherichia Coli Inorganic Pyrophosphatase Complexed with Ca(2+) or Capp(I) at Atomic Resolution and Their Mechanistic Implications. J.Mol.Biol. V. 314 633 2001.
ISSN: ISSN 0022-2836
PubMed: 11846572
DOI: 10.1006/JMBI.2001.5149