Sodium in PDB 3i4q: Structure of A Putative Inorganic Pyrophosphatase From the Oil- Degrading Bacterium Oleispira Antarctica

All present enzymatic activity of Structure of A Putative Inorganic Pyrophosphatase From the Oil- Degrading Bacterium Oleispira Antarctica:
3.6.1.1;

The structure of Structure of A Putative Inorganic Pyrophosphatase From the Oil- Degrading Bacterium Oleispira Antarctica, PDB code: 3i4q was solved by A.U.Singer, E.Evdokimova, O.Kagan, A.M.Edwards, A.Joachimiak, A.Savchenko, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.56 / 1.63
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	110.666, 110.666, 74.324, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 21.2

The binding sites of Sodium atom in the Structure of A Putative Inorganic Pyrophosphatase From the Oil- Degrading Bacterium Oleispira Antarctica (pdb code 3i4q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of A Putative Inorganic Pyrophosphatase From the Oil- Degrading Bacterium Oleispira Antarctica, PDB code: 3i4q:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of A Putative Inorganic Pyrophosphatase From the Oil- Degrading Bacterium Oleispira Antarctica


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Putative Inorganic Pyrophosphatase From the Oil- Degrading Bacterium Oleispira Antarctica within 5.0Å range: probe atom residue distance (Å) B Occ A:Na176 b:22.6 occ:1.00 O A:HOH245 2.3 26.6 1.0 OD1 A:ASP103 2.3 23.6 1.0 OD2 A:ASP66 2.4 32.9 1.0 OD2 A:ASP71 2.4 20.2 1.0 O A:HOH268 2.4 25.2 1.0 O A:HOH206 2.5 19.0 1.0 O A:HOH331 3.2 16.5 1.0 CG A:ASP103 3.3 22.6 1.0 CG A:ASP71 3.3 17.0 1.0 CG A:ASP66 3.4 34.5 1.0 OD2 A:ASP103 3.6 23.6 1.0 OD1 A:ASP66 3.7 33.6 1.0 NZ A:LYS105 3.9 21.1 1.0 OD1 A:ASP71 4.0 17.6 1.0 O A:GLU104 4.0 16.4 0.5 O A:HOH289 4.1 37.0 1.0 CB A:ASP71 4.2 13.8 1.0 O A:GLU104 4.2 17.2 0.5 OE2 A:GLU104 4.3 14.8 0.5 O A:ALA69 4.4 17.6 1.0 O A:HOH237 4.4 31.4 1.0 CB A:ALA64 4.5 24.3 1.0 N A:ASP71 4.5 13.2 1.0 CB A:ASP103 4.6 23.2 1.0 CB A:ASP66 4.7 34.0 1.0 N A:GLU104 4.7 19.4 0.5 N A:GLU104 4.7 19.9 0.5 CA A:ASP103 4.9 22.6 1.0 O A:HOH243 4.9 29.1 1.0 CE A:LYS105 5.0 21.2 1.0

Sodium binding site 2 out of 2 in the Structure of A Putative Inorganic Pyrophosphatase From the Oil- Degrading Bacterium Oleispira Antarctica


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Putative Inorganic Pyrophosphatase From the Oil- Degrading Bacterium Oleispira Antarctica within 5.0Å range: probe atom residue distance (Å) B Occ A:Na177 b:46.8 occ:1.00 O A:GLU146 2.3 25.3 1.0 O A:LYS149 2.4 43.6 1.0 O A:HOH346 2.4 34.3 1.0 O A:LYS143 2.8 15.2 1.0 C A:GLU146 3.4 24.9 1.0 C A:LYS149 3.5 43.6 1.0 N A:LYS149 3.6 43.6 1.0 O A:ASP144 3.6 19.9 1.0 C A:ASP144 3.9 17.4 1.0 N A:GLU146 4.0 23.2 1.0 C A:LYS143 4.0 16.2 1.0 CA A:LYS149 4.1 43.8 1.0 CA A:GLU146 4.2 24.3 1.0 CA A:ASP144 4.3 16.1 1.0 N A:LEU145 4.5 18.1 1.0 N A:TRP150 4.5 43.6 1.0 CB A:LYS149 4.6 44.0 1.0 C A:GLY148 4.6 43.5 1.0 CB A:GLU146 4.6 24.6 1.0 C A:LEU145 4.6 21.7 1.0 N A:GLY148 4.7 42.8 1.0 N A:ASP144 4.7 15.3 1.0 CA A:GLY148 4.7 43.1 1.0 CA A:TRP150 4.8 43.4 1.0 CA A:LEU145 4.9 19.1 1.0

M.Kube, T.N.Chernikova, Y.Al-Ramahi, A.Beloqui, N.Lopez-Cortez, M.E.Guazzaroni, H.J.Heipieper, S.Klages, O.R.Kotsyurbenko, I.Langer, T.Y.Nechitaylo, H.Lunsdorf, M.Fernandez, S.Juarez, S.Ciordia, A.Singer, O.Kagan, O.Egorova, P.Alain Petit, P.Stogios, Y.Kim, A.Tchigvintsev, R.Flick, R.Denaro, M.Genovese, J.P.Albar, O.N.Reva, M.Martinez-Gomariz, H.Tran, M.Ferrer, A.Savchenko, A.F.Yakunin, M.M.Yakimov, O.V.Golyshina, R.Reinhardt, P.N.Golyshin. Genome Sequence and Functional Genomic Analysis of the Oil-Degrading Bacterium Oleispira Antarctica. Nat Commun V. 4 2156 2013.
ISSN: ESSN 2041-1723
PubMed: 23877221
DOI: 10.1038/NCOMMS3156