Sodium in the structure of Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex With Sucrose (pdb 2qqv)

The binding sites of Sodium atom in the structure of Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex With Sucrose (pdb code 2qqv). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2qqv structure was solved by W.LAMMENS, K.LE ROY, A.VAN LAERE, A.RABIJNS, W.VAN DEN ENDE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.6-3.0 Space group P32 a (A) 107.131 b (A) 107.131 c (A) 50.832 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.9 Rfree (%) 23.7 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2qqv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2qqv. 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: Arg291, A: Lys321, A: Val336, A: Arg337, A: Glu338, conact list: Atom Atom Distance (A) Na CD A:Arg291 3.96 Na CZ A:Arg291 3.98 Na NE A:Arg291 4.42 Na NH1 A:Arg291 2.78 Na CB A:Lys321 4.23 Na CE A:Lys321 4.76 Na CD A:Lys321 3.95 Na CG A:Lys321 4.32 Na CB A:Val336 4.58 Na C A:Val336 4.29 Na CG1 A:Val336 4.63 Na CA A:Val336 4.05 Na N A:Arg337 3.50 Na CB A:Arg337 4.06 Na CG A:Arg337 3.63 Na CA A:Arg337 4.41 Na OE1 A:Glu338 4.60 interactive model: Sodium binding site 2 out of 2 in 2qqv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2qqv. 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: Ser85, A: Ala86, A: Thr87, A: Val95, A: Ile96, A: Leu97, A: Thr151, A: Thr152, A: Ala153, A: Phe183, conact list: Atom Atom Distance (A) Na O A:Ser85 3.46 Na N A:Ser85 4.97 Na CB A:Ser85 4.15 Na C A:Ser85 3.81 Na CA A:Ser85 4.52 Na O A:Ala86 4.71 Na N A:Ala86 4.21 Na C A:Ala86 4.04 Na CA A:Ala86 4.30 Na N A:Thr87 3.64 Na CB A:Thr87 3.75 Na CG2 A:Thr87 4.98 Na OG1 A:Thr87 2.59 Na CA A:Thr87 4.23 Na O A:Val95 4.47 Na C A:Ile96 4.99 Na N A:Leu97 4.08 Na CB A:Leu97 3.92 Na CD1 A:Leu97 3.95 Na CG A:Leu97 3.97 Na CA A:Leu97 4.61 Na O A:Thr151 3.03 Na C A:Thr151 3.96 Na N A:Thr152 4.25 Na CB A:Thr152 4.94 Na C A:Thr152 4.27 Na CA A:Thr152 3.80 Na N A:Ala153 3.85 Na CB A:Ala153 4.59 Na CA A:Ala153 4.85 Na CZ A:Phe183 4.91 interactive model: