Sodium in the structure of Crystal Structure of Moorella Thermoacetica Selb(377-511) (pdb 2v9v)

The binding sites of Sodium atom in the structure of Crystal Structure of Moorella Thermoacetica Selb(377-511) (pdb code 2v9v). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2v9v structure was solved by O.GANICHKIN, M.C.WAHL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.1 Space group C121 a (A) 65.349 b (A) 46.087 c (A) 58.683 alpha (°) 90.00 beta (°) 120.45 gamma (°) 90.00 Rfactor (%) 12 Rfree (%) 14.1 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2v9v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2v9v. 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: Asn430, A: Asp431, A: Hoh2005, A: Hoh2007, A: Hoh2016, A: Hoh2027, A: Hoh2037, conact list: Atom Atom Distance (A) Na HB2 A:Asn430 3.85 Na CB A:Asn430 3.93 Na HB3 A:Asn430 3.33 Na C A:Asn430 3.28 Na CA A:Asn430 4.22 Na O A:Asn430 2.33 Na HA A:Asn430 4.83 Na N A:Asp431 4.03 Na CB A:Asp431 4.56 Na HB3 A:Asp431 4.98 Na HA A:Asp431 3.50 Na OD2 A:Asp431 4.51 Na H A:Asp431 4.80 Na OD1 A:Asp431 2.73 Na CG A:Asp431 3.76 Na CA A:Asp431 4.14 Na O A:Hoh2005 4.49 Na O A:Hoh2007 4.81 Na O A:Hoh2016 3.41 Na O A:Hoh2027 4.61 Na O A:Hoh2037 2.49 interactive model: Sodium binding site 2 out of 2 in 2v9v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2v9v. 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: Thr424, A: Leu425, A: Leu426, A: Glu488, A: Hoh2003, A: Hoh2006, A: Hoh2038, A: Hoh2052, A: Hoh2058, conact list: Atom Atom Distance (A) Na HG22 A:Thr424 4.77 Na HA A:Thr424 4.86 Na HG23 A:Thr424 4.58 Na CG2 A:Thr424 4.44 Na HG21 A:Thr424 3.55 Na HB2 A:Leu425 3.82 Na N A:Leu425 3.95 Na CB A:Leu425 4.49 Na HB3 A:Leu425 4.94 Na C A:Leu425 3.44 Na CA A:Leu425 4.17 Na O A:Leu425 2.25 Na H A:Leu425 3.32 Na HB2 A:Leu426 4.78 Na HD21 A:Leu426 4.82 Na N A:Leu426 4.47 Na CA A:Leu426 4.67 Na HA A:Leu426 3.99 Na HD23 A:Leu426 4.86 Na OE1 A:Glu488 4.33 Na OE2 A:Glu488 4.56 Na CD A:Glu488 4.89 Na O A:Hoh2003 4.43 Na O A:Hoh2006 4.93 Na O A:Hoh2038 2.32 Na O A:Hoh2052 2.46 Na O A:Hoh2058 2.30 interactive model: