Sodium in the structure of Crystal Structure of the T. Thermophilus Dodecin W38F Mutant (pdb 2vyx)

The binding sites of Sodium atom in the structure of Crystal Structure of the T. Thermophilus Dodecin W38F Mutant (pdb code 2vyx). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2vyx structure was solved by L.-O.ESSEN, B.MEISSNER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.5 Space group P212121 a (A) 67.630 b (A) 98.550 c (A) 139.840 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.8 Rfree (%) 25 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2vyx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2vyx. 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: D: Thr47, D: Glu55, D: Gln57, I: Lys3, F: Fmn1070, F: Fmn1072, D: Hoh2013, D: Hoh2031, D: Hoh2038, D: Hoh2039, F: Hoh2043, F: Hoh2044, F: Hoh2050, conact list: Atom Atom Distance (A) Na CB D:Thr47 5.00 Na CG2 D:Thr47 4.16 Na OG1 D:Thr47 4.76 Na OE1 D:Glu55 3.90 Na OE2 D:Glu55 4.42 Na CD D:Glu55 4.39 Na NE2 D:Gln57 4.27 Na CE I:Lys3 4.76 Na NZ I:Lys3 3.96 Na O2 F:Fmn1070 3.92 Na C4' F:Fmn1072 3.98 Na O4' F:Fmn1072 4.30 Na C5' F:Fmn1072 4.03 Na O D:Hoh2013 4.30 Na O D:Hoh2031 2.79 Na O D:Hoh2038 4.38 Na O D:Hoh2039 2.53 Na O F:Hoh2043 4.19 Na O F:Hoh2044 3.02 Na O F:Hoh2050 4.16 interactive model: