Sodium in the structure of The Crystal Structure of Protein (XCC3681) From Xanthomonas Campestris Pv. Campestris Str. Atcc 33913 (pdb 3hiu)

The binding sites of Sodium atom in the structure of The Crystal Structure of Protein (XCC3681) From Xanthomonas Campestris Pv. Campestris Str. Atcc 33913 (pdb code 3hiu). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3hiu structure was solved by K.TAN, X.XU, H.CUI, A.SAVCHENKO, A.EDWARDS, A.JOACHIMIAK, MIDWESTCENTER FOR STRUCTURAL GENOMICS (MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 49.7-1.9 Space group P1211 a (A) 102.592 b (A) 56.843 c (A) 53.990 alpha (°) 90.00 beta (°) 90.01 gamma (°) 90.00 Rfactor (%) 20.7 Rfree (%) 25.7 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3hiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3hiu. 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: Glu21, A: Ala24, A: Mse28, A: His48, A: Thr52, A: Gln55, A: Glu107, A: Glu110, A: Glu140, conact list: Atom Atom Distance (A) Na OE1 A:Glu21 2.78 Na OE2 A:Glu21 3.74 Na CD A:Glu21 3.64 Na CB A:Ala24 4.14 Na CE A:Mse28 4.77 Na NE2 A:His48 3.61 Na CD2 A:His48 4.29 Na CE1 A:His48 4.24 Na CB A:Thr52 4.09 Na CG2 A:Thr52 4.72 Na OG1 A:Thr52 2.73 Na CA A:Thr52 4.57 Na NE2 A:Gln55 4.04 Na OE1 A:Gln55 2.78 Na CD A:Gln55 3.75 Na OE1 A:Glu107 4.54 Na OE2 A:Glu107 4.00 Na CD A:Glu107 4.71 Na OE1 A:Glu110 2.76 Na OE2 A:Glu110 2.85 Na CD A:Glu110 3.18 Na CG A:Glu110 4.69 Na OE1 A:Glu140 3.65 Na OE2 A:Glu140 3.05 Na CD A:Glu140 3.67 interactive model: Sodium binding site 2 out of 4 in 3hiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3hiu. 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: Glu21, B: Ala24, B: Mse28, B: His48, B: Thr52, B: Gln55, B: Glu107, B: Glu110, B: Glu140, conact list: Atom Atom Distance (A) Na OE1 B:Glu21 3.03 Na OE2 B:Glu21 4.17 Na CD B:Glu21 3.99 Na CB B:Ala24 4.29 Na SE B:Mse28 4.97 Na CE B:Mse28 4.57 Na NE2 B:His48 3.14 Na ND1 B:His48 4.45 Na CD2 B:His48 3.96 Na CE1 B:His48 3.55 Na CG B:His48 4.69 Na N B:Thr52 4.84 Na CB B:Thr52 3.80 Na CG2 B:Thr52 4.28 Na OG1 B:Thr52 2.56 Na CA B:Thr52 4.20 Na NE2 B:Gln55 3.79 Na OE1 B:Gln55 2.82 Na CD B:Gln55 3.64 Na OE1 B:Glu107 4.59 Na OE2 B:Glu107 4.68 Na OE1 B:Glu110 3.23 Na OE2 B:Glu110 3.25 Na CD B:Glu110 3.64 Na OE1 B:Glu140 3.43 Na OE2 B:Glu140 3.41 Na CD B:Glu140 3.77 interactive model: Sodium binding site 3 out of 4 in 3hiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3hiu. 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: C: Glu21, C: Thr52, C: Gln55, C: Glu110, C: Tyr114, C: Ile136, C: Glu140, C: Hoh208, conact list: Atom Atom Distance (A) Na OE1 C:Glu21 2.69 Na OE2 C:Glu21 2.77 Na CD C:Glu21 3.08 Na CG C:Glu21 4.57 Na CG2 C:Thr52 4.64 Na OG1 C:Thr52 4.73 Na NE2 C:Gln55 3.67 Na OE1 C:Gln55 2.63 Na CB C:Gln55 4.71 Na CD C:Gln55 3.37 Na CG C:Gln55 4.57 Na OE1 C:Glu110 2.42 Na CB C:Glu110 4.81 Na OE2 C:Glu110 3.92 Na CD C:Glu110 3.50 Na CG C:Glu110 4.75 Na CE2 C:Tyr114 4.13 Na CZ C:Tyr114 4.72 Na OH C:Tyr114 4.43 Na CG2 C:Ile136 3.96 Na OE1 C:Glu140 3.46 Na CB C:Glu140 4.77 Na OE2 C:Glu140 2.91 Na CD C:Glu140 2.93 Na CG C:Glu140 3.22 Na O C:Hoh208 2.92 interactive model: Sodium binding site 4 out of 4 in 3hiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3hiu. 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: Glu21, D: Thr52, D: Gln55, D: Glu110, D: Tyr114, D: Ile136, D: Glu140, D: Hoh215, conact list: Atom Atom Distance (A) Na OE1 D:Glu21 2.64 Na OE2 D:Glu21 2.79 Na CD D:Glu21 3.07 Na CG D:Glu21 4.57 Na CB D:Thr52 4.70 Na CG2 D:Thr52 4.29 Na OG1 D:Thr52 4.11 Na NE2 D:Gln55 3.58 Na OE1 D:Gln55 2.47 Na CB D:Gln55 4.64 Na CD D:Gln55 3.25 Na CG D:Gln55 4.48 Na OE1 D:Glu110 2.49 Na OE2 D:Glu110 3.91 Na CD D:Glu110 3.55 Na CG D:Glu110 4.87 Na CE2 D:Tyr114 4.26 Na CZ D:Tyr114 4.77 Na OH D:Tyr114 4.42 Na CG2 D:Ile136 3.97 Na OE1 D:Glu140 3.50 Na CB D:Glu140 4.91 Na OE2 D:Glu140 2.85 Na CD D:Glu140 2.97 Na CG D:Glu140 3.38 Na O D:Hoh215 3.20 interactive model: