Sodium in PDB 6n1c: Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1

All present enzymatic activity of Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1:
3.6.1.1;

The structure of Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1, PDB code: 6n1c was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.97 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.080, 119.940, 74.900, 90.00, 109.59, 90.00
R / Rfree (%)	19.3 / 23.2

The binding sites of Sodium atom in the Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1 (pdb code 6n1c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1, PDB code: 6n1c:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1


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 Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:52.1 occ:1.00 O A:HOH303 2.3 47.7 1.0 O A:LYS149 2.4 45.2 1.0 O A:HOH393 2.4 40.4 1.0 O A:GLU146 2.5 33.4 1.0 O A:LYS143 2.6 35.7 1.0 O A:HOH373 2.7 44.0 1.0 C A:GLU146 3.4 37.2 1.0 O A:ASP144 3.6 37.0 1.0 C A:LYS149 3.6 43.5 1.0 C A:LYS143 3.7 39.8 1.0 C A:ASP144 3.8 34.3 1.0 N A:GLU146 3.8 33.4 1.0 N A:LYS149 3.9 40.2 1.0 CA A:ASP144 4.0 34.0 1.0 O A:HOH313 4.1 60.5 1.0 CA A:GLU146 4.1 32.9 1.0 CA A:LYS149 4.2 40.2 1.0 N A:ASP144 4.4 35.9 1.0 O A:HOH343 4.4 47.5 1.0 N A:GLU147 4.4 32.6 1.0 N A:LEU145 4.4 29.3 1.0 N A:GLY148 4.5 46.5 1.0 CB A:GLU146 4.5 30.9 1.0 CA A:GLU147 4.6 47.9 1.0 CB A:LYS149 4.6 45.8 1.0 C A:LEU145 4.6 36.8 1.0 N A:TRP150 4.6 37.6 1.0 C A:GLU147 4.8 43.6 1.0 CB A:LYS143 4.8 39.9 1.0 CA A:TRP150 4.9 36.6 1.0 CA A:LYS143 4.9 33.2 1.0 CA A:LEU145 4.9 34.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1


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 Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:66.6 occ:1.00 O A:HOH305 2.5 46.0 1.0 OE2 A:GLU146 2.6 72.5 1.0 OE1 A:GLU146 2.7 64.5 1.0 O F:HOH338 2.7 54.2 1.0 CD A:GLU146 3.0 61.9 1.0 O A:HOH322 3.1 47.9 1.0 O F:LEU114 3.8 41.5 1.0 O A:PHE45 3.8 34.7 1.0 CG2 A:THR47 3.9 32.7 1.0 O F:HOH328 4.1 50.4 1.0 CB A:ARG44 4.1 36.4 1.0 CD A:ARG44 4.2 51.6 1.0 CG A:GLU146 4.5 40.2 1.0 CG A:ARG44 4.5 45.2 1.0 C F:LEU114 4.6 41.5 1.0 O F:HOH332 4.6 36.3 1.0 CA F:SER115 4.7 35.3 1.0 O F:LYS113 4.7 54.8 1.0 OG1 A:THR47 4.8 29.4 1.0 N A:PHE45 4.9 36.0 1.0 O A:HOH369 4.9 69.7 1.0 C A:PHE45 5.0 36.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:69.0 occ:1.00 O D:HOH334 2.3 56.4 1.0 O D:ALA104 2.5 54.1 1.0 OD2 D:ASP103 2.5 47.6 1.0 O D:HOH377 2.6 64.3 1.0 OD2 D:ASP71 3.0 64.2 1.0 O D:HOH317 3.4 60.8 1.0 NZ D:LYS105 3.4 43.5 1.0 C D:ALA104 3.5 58.8 1.0 N D:ALA104 3.5 51.4 1.0 CG D:ASP103 3.7 53.6 1.0 CG D:ASP71 3.8 65.8 1.0 C D:ASP103 3.9 48.8 1.0 CA D:ASP103 4.0 42.6 1.0 CA D:ALA104 4.1 49.3 1.0 CB D:ASP71 4.2 62.0 1.0 OD2 D:ASP66 4.4 91.7 1.0 CD D:LYS105 4.4 50.4 1.0 CB D:ASP103 4.4 43.9 1.0 CE D:LYS105 4.5 42.5 1.0 N D:LYS105 4.6 52.7 1.0 OD1 D:ASP103 4.6 53.5 1.0 O D:ASP103 4.8 58.9 1.0 OD1 D:ASP71 4.8 70.0 1.0 CG D:LYS105 4.8 51.7 1.0 N D:ASP71 4.9 54.3 1.0 CB D:ALA104 4.9 50.5 1.0 CA D:LYS105 5.0 48.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na202 b:41.5 occ:1.00 O F:LYS149 2.2 51.7 1.0 O F:HOH353 2.3 45.6 1.0 O F:GLU146 2.3 50.9 1.0 O F:HOH322 2.4 40.5 1.0 O F:LYS143 2.9 48.0 1.0 C F:GLU146 3.3 50.2 1.0 C F:LYS149 3.4 51.7 1.0 N F:GLU146 3.9 51.4 1.0 O F:ASP144 4.0 50.6 1.0 N F:LYS149 4.0 52.8 1.0 C F:LYS143 4.0 46.7 1.0 CA F:GLU146 4.1 52.9 1.0 C F:ASP144 4.2 48.9 1.0 N F:GLU147 4.3 51.3 1.0 CA F:LYS149 4.3 51.5 1.0 N F:TRP150 4.4 55.2 1.0 CA F:GLU147 4.4 53.5 1.0 CB F:GLU146 4.4 48.8 1.0 OE2 F:GLU147 4.4 57.5 1.0 CA F:TRP150 4.5 53.6 1.0 N F:GLY148 4.5 55.3 1.0 CA F:ASP144 4.6 48.4 1.0 CB F:TRP150 4.6 54.6 1.0 C F:GLU147 4.7 53.9 1.0 O F:HOH356 4.8 56.8 1.0 CB F:LYS149 4.8 54.3 1.0 N F:LEU145 4.8 50.4 1.0 N F:ASP144 4.8 46.7 1.0 C F:LEU145 4.8 48.0 1.0 CB F:LYS143 4.8 53.2 1.0

J.Abendroth, S.J.Mayclin, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Inorganic Pyrophosphatase From Legionella Pneumophila Philadelphia 1 To Be Published.