Sodium in PDB 2o5w: Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate

The structure of Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate, PDB code: 2o5w was solved by S.B.Gabelli, M.A.Bianchet, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	124.416, 42.909, 108.328, 90.00, 115.19, 90.00
R / Rfree (%)	19.5 / 28.7

The structure of Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate also contains other interesting chemical elements:

Samarium

(Sm)

3 atoms

The binding sites of Sodium atom in the Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate (pdb code 2o5w). 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 the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate, PDB code: 2o5w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na171 b:44.8 occ:1.00 OPP A:PPV163 2.2 78.5 1.0 OE2 A:GLU60 2.5 42.5 1.0 O A:THR40 2.6 22.5 1.0 SM A:SM170 2.9 76.7 1.0 P1 A:PPV163 3.0 79.5 1.0 O11 A:PPV163 3.1 79.1 1.0 OE1 A:GLU56 3.2 34.8 1.0 O22 A:PPV163 3.2 77.3 1.0 P2 A:PPV163 3.3 77.2 1.0 O31 A:PPV163 3.3 79.1 1.0 CD A:GLU60 3.5 41.2 1.0 C A:THR40 3.7 22.3 1.0 CD A:GLU56 3.9 34.7 1.0 CA A:GLY41 3.9 23.3 1.0 O12 A:PPV163 3.9 77.4 1.0 OE1 A:GLU117 4.0 41.8 1.0 OE2 A:GLU56 4.0 34.6 1.0 CG A:GLU60 4.1 39.3 1.0 N A:GLY41 4.2 22.8 1.0 O21 A:PPV163 4.4 79.7 1.0 OE1 A:GLU60 4.5 41.5 1.0 O32 A:PPV163 4.5 77.0 1.0 OG1 A:THR40 4.5 21.6 1.0 CA A:THR40 4.8 22.0 1.0 N A:THR40 5.0 21.7 1.0

Sodium binding site 2 out of 2 in the Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na171 b:53.1 occ:1.00 OE2 C:GLU60 2.2 46.4 1.0 O31 C:PPV163 2.2 65.3 1.0 O C:THR40 2.5 28.9 1.0 O22 C:PPV163 2.8 71.4 1.0 SM C:SM170 2.9 77.0 1.0 CD C:GLU60 3.4 43.1 1.0 P1 C:PPV163 3.4 70.1 1.0 OE1 C:GLU117 3.4 47.7 1.0 OE1 C:GLU56 3.5 47.5 1.0 C C:THR40 3.6 28.8 1.0 O11 C:PPV163 3.6 69.4 1.0 P2 C:PPV163 3.7 71.6 1.0 O32 C:PPV163 3.9 71.7 1.0 CA C:GLY41 3.9 30.4 1.0 CG C:GLU60 3.9 40.1 1.0 OPP C:PPV163 4.0 70.5 1.0 N C:GLY41 4.2 29.4 1.0 OG1 C:THR40 4.3 28.4 1.0 OE1 C:GLU60 4.4 43.5 1.0 CD C:GLU56 4.4 39.0 1.0 CD C:GLU117 4.6 47.3 1.0 O21 C:PPV163 4.6 69.6 1.0 CA C:THR40 4.7 28.1 1.0 N C:THR40 4.8 27.5 1.0 OE2 C:GLU56 4.9 38.9 1.0 OE2 C:GLU117 5.0 47.4 1.0

S.B.Gabelli, M.A.Bianchet, W.Xu, C.A.Dunn, Z.D.Niu, L.M.Amzel, M.J.Bessman. Structure and Function of the E. Coli Dihydroneopterin Triphosphate Pyrophosphatase: A Nudix Enzyme Involved in Folate Biosynthesis. Structure V. 15 1014 2007.
ISSN: ISSN 0969-2126
PubMed: 17698004
DOI: 10.1016/J.STR.2007.06.018