Sodium in the structure of X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex (pdb 3f7k)

The binding sites of Sodium atom in the structure of X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex (pdb code 3f7k). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3f7k structure was solved by D.S.SHIN, M.DIDONATO, D.P.BARONDEAU, E.D.GETZOFF, J.A.TAINER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 45.0-1.4 Space group P6122 a (A) 62.563 b (A) 62.563 c (A) 163.745 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 12.8 Rfree (%) 17.6 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3f7k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3f7k. 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: Ala87, A: Gly88, A: Glu89, A: Asp90, A: Gly91, A: Lys92, A: Hoh328, A: Hoh371, A: Hoh392, conact list: Atom Atom Distance (A) Na C A:Ala87 4.59 Na O A:Gly88 3.64 Na N A:Gly88 3.31 Na C A:Gly88 3.25 Na CA A:Gly88 2.99 Na N A:Glu89 3.75 Na C A:Glu89 4.29 Na CA A:Glu89 4.62 Na O A:Asp90 4.56 Na N A:Asp90 3.18 Na CB A:Asp90 3.36 Na OD2 A:Asp90 3.22 Na C A:Asp90 3.75 Na OD1 A:Asp90 1.36 Na CG A:Asp90 2.39 Na CA A:Asp90 3.54 Na N A:Gly91 3.67 Na C A:Gly91 4.51 Na CA A:Gly91 4.65 Na O A:Lys92 3.33 Na N A:Lys92 3.44 Na CB A:Lys92 4.05 Na C A:Lys92 4.09 Na CG A:Lys92 4.69 Na CA A:Lys92 4.02 Na O A:Hoh328 4.98 Na O A:Hoh371 4.03 Na O A:Hoh392 2.16 interactive model: