Sodium in the structure of Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex With Sm+3 and Pyrophosphate (pdb 2o5w)

The binding sites of Sodium atom in the structure of Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex With Sm+3 and Pyrophosphate (pdb code 2o5w). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2o5w structure was solved by S.B.GABELLI, M.A.BIANCHET, L.M.AMZEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.6 Space group C121 a (A) 124.416 b (A) 42.909 c (A) 108.328 alpha (°) 90.00 beta (°) 115.19 gamma (°) 90.00 Rfactor (%) 19.5 Rfree (%) 28.7 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2o5w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2o5w. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Thr40, A: Gly41, A: Glu56, A: Glu60, A: Glu117, A: Sm170, A: Ppv163, conact list: Atom Atom Distance (A) Na O A:Thr40 2.63 Na N A:Thr40 4.99 Na OG1 A:Thr40 4.54 Na C A:Thr40 3.68 Na CA A:Thr40 4.85 Na N A:Gly41 4.23 Na CA A:Gly41 3.90 Na OE1 A:Glu56 3.16 Na OE2 A:Glu56 4.02 Na CD A:Glu56 3.85 Na OE1 A:Glu60 4.49 Na OE2 A:Glu60 2.48 Na CD A:Glu60 3.52 Na CG A:Glu60 4.11 Na OE1 A:Glu117 3.98 Na SM A:Sm170 2.89 Na OPP A:Ppv163 2.24 Na P2 A:Ppv163 3.26 Na O22 A:Ppv163 3.23 Na O32 A:Ppv163 4.52 Na P1 A:Ppv163 2.98 Na O21 A:Ppv163 4.40 Na O11 A:Ppv163 3.08 Na O31 A:Ppv163 3.34 Na O12 A:Ppv163 3.94 interactive model: Sodium binding site 2 out of 2 in 2o5w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2o5w. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Thr40, C: Gly41, C: Glu56, C: Glu60, C: Glu117, C: Sm170, C: Ppv163, conact list: Atom Atom Distance (A) Na O C:Thr40 2.51 Na N C:Thr40 4.84 Na OG1 C:Thr40 4.25 Na C C:Thr40 3.58 Na CA C:Thr40 4.72 Na N C:Gly41 4.18 Na CA C:Gly41 3.93 Na OE1 C:Glu56 3.53 Na OE2 C:Glu56 4.94 Na CD C:Glu56 4.42 Na OE1 C:Glu60 4.35 Na OE2 C:Glu60 2.24 Na CD C:Glu60 3.35 Na CG C:Glu60 3.95 Na OE1 C:Glu117 3.43 Na OE2 C:Glu117 4.98 Na CD C:Glu117 4.57 Na SM C:Sm170 2.91 Na OPP C:Ppv163 4.00 Na P2 C:Ppv163 3.71 Na O22 C:Ppv163 2.81 Na O32 C:Ppv163 3.89 Na P1 C:Ppv163 3.38 Na O21 C:Ppv163 4.63 Na O11 C:Ppv163 3.60 Na O31 C:Ppv163 2.24 interactive model: