Samarium 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:

Sodium

(Na)

2 atoms

The binding sites of Samarium 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 Samarium atom.
In total 3 binding sites of Samarium where determined in the Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate, PDB code: 2o5w:
Jump to Samarium binding site number: 1; 2; 3;

Samarium binding site 1 out of 3 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 Samarium with other atoms in the Sm 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:Sm170 b:76.7 occ:1.00 OE1 A:GLU56 2.7 34.8 1.0 OE2 A:GLU56 2.7 34.6 1.0 NA A:NA171 2.9 44.8 1.0 CD A:GLU56 3.0 34.7 1.0 OE1 A:GLU117 3.0 41.8 1.0 OE1 A:GLU59 3.2 38.2 1.0 O31 A:PPV163 3.6 79.1 1.0 CD A:GLU117 3.8 41.7 1.0 O11 A:PPV163 3.9 79.1 1.0 OE2 A:GLU117 3.9 42.3 1.0 CG A:GLU60 3.9 39.3 1.0 OE2 A:GLU60 4.1 42.5 1.0 P1 A:PPV163 4.2 79.5 1.0 CD A:GLU59 4.4 38.2 1.0 CD A:GLU60 4.4 41.2 1.0 OPP A:PPV163 4.4 78.5 1.0 CG A:GLU56 4.5 34.6 1.0 O A:THR40 4.6 22.5 1.0 CB A:GLU59 4.7 37.3 1.0 NH1 A:ARG55 4.9 31.6 1.0

Samarium binding site 2 out of 3 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 Samarium with other atoms in the Sm 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 B:Sm170 b:87.5 occ:1.00 OE2 B:GLU56 3.0 31.0 1.0 OE2 B:GLU117 3.1 52.0 1.0 OE1 B:GLU117 3.1 50.9 1.0 OE1 B:GLU56 3.1 32.0 1.0 OE2 B:GLU60 3.4 36.8 1.0 OE1 B:GLU59 3.4 35.8 1.0 CD B:GLU56 3.4 31.4 1.0 CD B:GLU117 3.5 50.7 1.0 CG B:GLU60 3.9 34.0 1.0 CD B:GLU60 4.1 35.9 1.0 CD B:GLU59 4.2 35.6 1.0 CB B:GLU59 4.4 34.7 1.0 O B:THR40 4.5 21.3 1.0 NH1 B:ARG55 4.6 24.7 1.0 CG B:GLU59 4.9 35.1 1.0 CG B:GLU56 4.9 31.8 1.0 OE2 B:GLU59 5.0 36.2 1.0

Samarium binding site 3 out of 3 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 Samarium with other atoms in the Sm binding site number 3 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:Sm170 b:77.0 occ:1.00 OE1 C:GLU56 2.3 47.5 1.0 NA C:NA171 2.9 53.1 1.0 OE1 C:GLU117 3.2 47.7 1.0 CD C:GLU56 3.3 39.0 1.0 OE2 C:GLU117 3.3 47.4 1.0 OE1 C:GLU59 3.3 39.5 1.0 OE2 C:GLU56 3.5 38.9 1.0 O31 C:PPV163 3.6 65.3 1.0 CD C:GLU117 3.6 47.3 1.0 CG C:GLU60 4.1 40.1 1.0 OE2 C:GLU60 4.1 46.4 1.0 CD C:GLU59 4.2 39.3 1.0 O11 C:PPV163 4.3 69.4 1.0 CB C:GLU59 4.4 36.9 1.0 O C:THR40 4.4 28.9 1.0 P1 C:PPV163 4.5 70.1 1.0 CD C:GLU60 4.5 43.1 1.0 CG C:GLU56 4.6 36.9 1.0 NH1 C:ARG55 4.8 26.6 1.0 OE2 C:GLU59 5.0 39.4 1.0 CG C:GLU59 5.0 37.5 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