Sodium in the structure of Crystal Structure of Trehalose-6-Phosphate Phosphatase Related Protein (pdb 1u02)

The binding sites of Sodium atom in the structure of Crystal Structure of Trehalose-6-Phosphate Phosphatase Related Protein (pdb code 1u02). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1u02 structure was solved by N.R.KRISHNAMURTHY, D.KUMARAN, S.SWAMINATHAN, S.K.BURLEY, NEW YORK SGXRESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.9 Space group C121 a (A) 117.995 b (A) 45.056 c (A) 53.391 alpha (°) 90.00 beta (°) 90.65 gamma (°) 90.00 Rfactor (%) 19.7 Rfree (%) 21.6 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1u02 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1u02. 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: Asp9, A: Gly10, A: Val13, A: Pro14, A: Ile15, A: Ile16, A: Pro19, A: Ser22, A: Arg47, A: Gol251, A: Hoh275, A: Hoh296, conact list: Atom Atom Distance (A) Na CB A:Asp9 3.90 Na OD2 A:Asp9 4.65 Na OD1 A:Asp9 2.66 Na CG A:Asp9 3.58 Na CA A:Asp9 4.33 Na N A:Gly10 4.92 Na CB A:Val13 4.95 Na CG2 A:Val13 3.97 Na O A:Pro14 2.89 Na C A:Pro14 3.93 Na N A:Ile15 4.39 Na CD1 A:Ile15 4.60 Na C A:Ile15 4.48 Na CA A:Ile15 3.96 Na N A:Ile16 4.07 Na CD1 A:Ile16 4.84 Na CG1 A:Ile16 4.19 Na CA A:Pro19 4.96 Na CB A:Ser22 3.60 Na OG A:Ser22 2.73 Na CA A:Ser22 4.94 Na NH2 A:Arg47 3.79 Na O2 A:Gol251 4.42 Na C2 A:Gol251 4.94 Na O A:Hoh275 3.52 Na O A:Hoh296 2.53 interactive model: Sodium binding site 2 out of 2 in 1u02 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1u02. 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: Gly10, A: Val13, A: Pro14, A: Val198, A: Asp211, A: Tyr212, A: Hoh286, A: Hoh381, A: Hoh423, conact list: Atom Atom Distance (A) Na O A:Gly10 3.41 Na C A:Gly10 4.08 Na CA A:Gly10 4.36 Na O A:Val13 4.84 Na CA A:Pro14 4.60 Na CG1 A:Val198 4.29 Na O A:Asp211 4.93 Na CB A:Asp211 3.61 Na C A:Asp211 3.79 Na CG A:Asp211 4.98 Na CA A:Asp211 3.64 Na N A:Tyr212 3.09 Na CB A:Tyr212 3.82 Na CE2 A:Tyr212 4.76 Na CD2 A:Tyr212 3.67 Na CG A:Tyr212 4.23 Na CA A:Tyr212 4.01 Na O A:Hoh286 2.98 Na O A:Hoh381 3.45 Na O A:Hoh423 2.17 interactive model: