Sodium in the structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex With Nitrite (pdb 3d1i)

The binding sites of Sodium atom in the structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex With Nitrite (pdb code 3d1i). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3d1i structure was solved by K.M.POLYAKOV, K.M.BOYKO, A.SLUTSKY, T.V.TIKHONOVA, A.N.ANTIPOV, R.A.ZVYAGILSKAYA, A.N.POPOV, V.S.LAMZIN, G.P.BOURENKOV, V.O.POPOV, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 12.0-1.8 Space group P213 a (A) 193.412 b (A) 193.412 c (A) 193.412 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 14.8 Rfree (%) 16.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3d1i Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3d1i. 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: Lys102, A: Asp450, A: Hoh1321, A: Hoh1363, A: Hoh1365, A: Hoh1404, A: Hoh1405, A: Hoh1448, conact list: Atom Atom Distance (A) Na HZ3 A:Lys102 4.67 Na HZ2 A:Lys102 4.15 Na NZ A:Lys102 4.72 Na HZ1 A:Lys102 4.85 Na OD2 A:Asp450 4.07 Na CG A:Asp450 4.95 Na O A:Hoh1321 4.92 Na O A:Hoh1363 4.60 Na O A:Hoh1365 3.74 Na O A:Hoh1404 2.30 Na O A:Hoh1405 2.36 Na O A:Hoh1448 4.74 interactive model: Sodium binding site 2 out of 2 in 3d1i Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3d1i. 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: B: Lys102, B: Asp450, B: Hoh1783, B: Hoh1822, B: Hoh1824, B: Hoh1863, B: Hoh1864, B: Hoh1907, B: Hoh1908, B: Hoh1994, conact list: Atom Atom Distance (A) Na HZ3 B:Lys102 4.40 Na HZ2 B:Lys102 3.91 Na HZ2 B:Lys102 4.93 Na NZ B:Lys102 4.52 Na HZ1 B:Lys102 4.81 Na OD2 B:Asp450 3.71 Na CG B:Asp450 4.68 Na O B:Hoh1783 4.76 Na O B:Hoh1822 4.67 Na O B:Hoh1824 3.84 Na O B:Hoh1863 2.11 Na O B:Hoh1864 2.32 Na O B:Hoh1907 4.58 Na O B:Hoh1908 4.81 Na O B:Hoh1994 2.51 interactive model: