Sodium in the structure of Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose (pdb 2qw1)

The binding sites of Sodium atom in the structure of Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose (pdb code 2qw1). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2qw1 structure was solved by M.J.BORROK, L.L.KIESSLING, K.T.FOREST, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-1.7 Space group P212121 a (A) 56.930 b (A) 74.660 c (A) 110.070 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18 Rfree (%) 20.4 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2qw1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2qw1. 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: Asn91, A: Thr110, A: Asp111, A: Ser112, A: Asn256, A: Tyr295, A: Hoh339, A: Hoh349, A: Hoh357, A: Hoh359, A: Hoh383, A: Hoh428, A: Hoh429, A: Hoh603, conact list: Atom Atom Distance (A) Na OD1 A:Asn91 4.08 Na O A:Thr110 2.45 Na N A:Thr110 4.01 Na CB A:Thr110 4.16 Na OG1 A:Thr110 4.94 Na C A:Thr110 3.58 Na CA A:Thr110 4.14 Na O A:Asp111 4.73 Na N A:Asp111 4.69 Na C A:Asp111 4.50 Na CA A:Asp111 4.99 Na N A:Ser112 4.44 Na CA A:Ser112 4.69 Na ND2 A:Asn256 4.23 Na OD1 A:Asn256 4.42 Na CG A:Asn256 4.74 Na CE2 A:Tyr295 4.70 Na CZ A:Tyr295 3.66 Na CE1 A:Tyr295 4.09 Na OH A:Tyr295 2.62 Na O A:Hoh339 2.51 Na O A:Hoh349 4.31 Na O A:Hoh357 4.64 Na O A:Hoh359 4.84 Na O A:Hoh383 4.92 Na O A:Hoh428 2.21 Na O A:Hoh429 2.49 Na O A:Hoh603 2.44 interactive model: Sodium binding site 2 out of 2 in 2qw1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2qw1. 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: Leu222, A: Lys227, A: Ser228, A: Ser229, A: Ile230, A: Pro231, A: Val232, A: Gly248, A: Ala249, A: Hoh392, A: Hoh412, A: Hoh413, A: Hoh414, A: Hoh415, A: Hoh510, A: Hoh539, conact list: Atom Atom Distance (A) Na CD1 A:Leu222 4.85 Na O A:Lys227 4.99 Na O A:Ser228 2.30 Na CB A:Ser228 4.85 Na C A:Ser228 3.40 Na CA A:Ser228 4.19 Na O A:Ser229 4.50 Na N A:Ser229 4.34 Na C A:Ser229 4.09 Na CA A:Ser229 4.48 Na O A:Ile230 2.32 Na N A:Ile230 3.94 Na C A:Ile230 3.21 Na CA A:Ile230 4.21 Na N A:Pro231 3.88 Na C A:Pro231 4.49 Na CA A:Pro231 3.86 Na N A:Val232 4.42 Na CG2 A:Val232 4.58 Na O A:Gly248 4.76 Na O A:Ala249 3.79 Na C A:Ala249 4.59 Na O A:Hoh392 4.10 Na O A:Hoh412 2.39 Na O A:Hoh413 2.68 Na O A:Hoh414 2.26 Na O A:Hoh415 2.64 Na O A:Hoh510 4.85 Na O A:Hoh539 4.58 interactive model: