Sodium in PDB 2au6: Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase

All present enzymatic activity of Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase:
3.6.1.1;

The structure of Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase, PDB code: 2au6 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 / 1.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	110.805, 110.805, 73.576, 90.00, 90.00, 120.00
R / Rfree (%)	12.5 / 15.7

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

Fluorine	(F)	1 atom
Manganese	(Mn)	6 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase (pdb code 2au6). 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 Structure of Catalytic Intermediate of Inorganic Pyrophosphatase, PDB code: 2au6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Catalytic Intermediate 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 Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:17.0 occ:1.00 O A:LYS148 2.3 17.5 1.0 O A:GLU145 2.3 16.0 1.0 O A:HOH476 2.5 25.7 1.0 O A:HOH335 2.5 23.3 1.0 O A:LYS142 2.5 14.8 1.0 O A:HOH392 2.7 24.4 1.0 C A:GLU145 3.3 15.5 1.0 C A:LYS148 3.4 16.1 1.0 C A:LYS142 3.6 14.5 1.0 N A:LYS148 3.9 17.9 1.0 N A:GLU145 3.9 16.2 1.0 CA A:GLU145 4.1 16.8 1.0 O A:ASP143 4.1 18.1 1.0 C A:ASP143 4.1 15.2 1.0 CA A:LYS148 4.1 18.7 1.0 N A:LYS146 4.2 20.3 1.0 CA A:ASP143 4.2 14.7 1.0 O A:HOH444 4.3 32.3 1.0 CA A:LYS146 4.3 19.8 1.0 O A:HOH362 4.3 19.9 1.0 N A:GLY147 4.3 19.6 1.0 N A:ASP143 4.4 14.2 1.0 CB A:LYS148 4.4 19.2 0.6 CB A:LYS142 4.4 16.6 1.0 CB A:LYS148 4.5 23.1 0.4 CB A:GLU145 4.5 18.1 0.3 CB A:GLU145 4.5 17.8 0.3 N A:TRP149 4.5 15.0 1.0 C A:LYS146 4.5 18.6 1.0 N A:LEU144 4.6 15.4 1.0 CA A:LYS142 4.6 14.6 1.0 CB A:GLU145 4.6 20.9 0.3 O A:HOH491 4.7 27.2 1.0 CA A:TRP149 4.7 15.8 1.0 C A:LEU144 4.8 18.3 1.0 C A:GLY147 4.9 21.5 1.0 CB A:TRP149 5.0 17.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:26.5 occ:0.85 MN A:MN205 2.5 33.9 0.2 O A:HOH477 2.5 20.9 0.4 O A:HOH355 2.8 32.5 0.5 O A:HOH588 3.0 19.8 0.6 O A:HOH587 4.1 42.6 1.0 O A:HOH324 4.2 40.6 0.7 OD1 A:ASP26 4.3 20.8 1.0 O A:HOH310 4.8 36.6 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