Sodium in PDB 3eiy: Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei with Bound Pyrophosphate

All present enzymatic activity of Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei with Bound Pyrophosphate:
3.6.1.1;

The structure of Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei with Bound Pyrophosphate, PDB code: 3eiy 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)	50.00 / 2.10
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	100.952, 100.952, 111.233, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 24.9

The structure of Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei with Bound Pyrophosphate also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei with Bound Pyrophosphate (pdb code 3eiy). 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 Inorganic Pyrophosphatase From Burkholderia Pseudomallei with Bound Pyrophosphate, PDB code: 3eiy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei with Bound Pyrophosphate


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 Burkholderia Pseudomallei with Bound Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na177 b:26.7 occ:1.00 O3 A:POP179 2.2 30.5 1.0 O A:HOH201 2.5 27.8 1.0 O6 A:POP179 2.6 33.1 1.0 OD2 A:ASP103 2.6 38.1 1.0 OD2 A:ASP98 2.6 44.8 1.0 O A:HOH257 2.7 44.2 1.0 P1 A:POP179 3.5 32.7 1.0 NZ A:LYS143 3.5 31.7 1.0 CG A:ASP103 3.6 40.2 1.0 P2 A:POP179 3.7 36.0 1.0 O A:HOH239 3.8 37.1 1.0 NZ A:LYS105 3.8 23.0 1.0 CG A:ASP98 3.8 45.8 1.0 O2 A:POP179 4.0 33.5 1.0 O A:POP179 4.0 33.5 1.0 O A:HOH231 4.0 31.6 1.0 OD1 A:ASP103 4.2 42.3 1.0 OH A:TYR142 4.3 23.2 1.0 O5 A:POP179 4.3 33.7 1.0 O A:HOH220 4.4 39.7 1.0 CE A:LYS105 4.5 24.9 1.0 CB A:ASP98 4.5 45.2 1.0 CB A:ASP103 4.5 39.5 1.0 OD1 A:ASP98 4.7 45.4 1.0 O1 A:POP179 4.7 32.6 1.0 CE A:LYS143 4.7 32.5 1.0 O4 A:POP179 5.0 33.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei with Bound Pyrophosphate


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 Burkholderia Pseudomallei with Bound Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na178 b:30.9 occ:1.00 O A:HOH263 2.5 45.2 1.0 OD1 A:ASP103 2.5 42.3 1.0 O A:HOH245 2.7 41.5 1.0 OD2 A:ASP71 2.8 28.4 1.0 O A:HOH247 2.9 33.8 1.0 O A:ALA104 2.9 30.2 1.0 OD2 A:ASP66 3.7 57.8 1.0 CG A:ASP103 3.8 40.2 1.0 CG A:ASP71 3.8 28.2 1.0 N A:ALA104 3.9 35.5 1.0 C A:ALA104 4.0 30.9 1.0 O A:HOH221 4.0 36.8 1.0 NZ A:LYS105 4.2 23.0 1.0 CB A:ASP71 4.2 26.4 1.0 CA A:ASP103 4.2 39.4 1.0 O A:HOH277 4.3 45.5 1.0 C A:ASP103 4.3 37.8 1.0 O A:HOH257 4.5 44.2 1.0 OG A:SER64 4.6 42.7 1.0 CA A:ALA104 4.6 32.8 1.0 CB A:ASP103 4.6 39.5 1.0 CG A:LYS105 4.6 27.0 1.0 OD2 A:ASP103 4.6 38.1 1.0 N A:ASP71 4.7 26.5 1.0 CG A:ASP66 4.7 54.2 1.0 OD1 A:ASP71 4.8 31.0 1.0 N A:LYS105 5.0 29.6 1.0

W.C.Van Voorhis, W.G.Hol, P.J.Myler, L.J.Stewart. The Role of Medical Structural Genomics in Discovering New Drugs For Infectious Diseases. Plos Comput Biol V. 5 00530 2009.
PubMed: 19855826
DOI: 10.1371/JOURNAL.PCBI.1000530