Sodium in the structure of X-Ray Crystal Structure of Rattlesnake Venom Complexed With Thiodigalactoside (pdb 1muq)

The binding sites of Sodium atom in the structure of X-Ray Crystal Structure of Rattlesnake Venom Complexed With Thiodigalactoside (pdb code 1muq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1muq structure was solved by J.R.WALKER, B.NAGAR, N.M.YOUNG, T.HIRAMA, J.M.RINI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 35.1-2.3 Space group C2221 a (A) 110.454 b (A) 151.234 c (A) 95.014 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21 Rfree (%) 25.7 Sodium Binding Sites: Sodium binding site 1 out of 5 in 1muq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1muq. 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: Leu13, A: Tyr15, A: Ala41, A: Ser42, A: Phe43, A: His44, A: Glu48, A: Asp83, A: Gln132, A: Hoh306, A: Hoh308, conact list: Atom Atom Distance (A) Na CD1 A:Leu13 4.02 Na CE2 A:Tyr15 3.95 Na CZ A:Tyr15 3.76 Na OH A:Tyr15 2.68 Na C A:Ala41 4.79 Na O A:Ser42 2.25 Na N A:Ser42 3.58 Na CB A:Ser42 3.66 Na OG A:Ser42 2.57 Na C A:Ser42 3.11 Na CA A:Ser42 3.69 Na N A:Phe43 4.11 Na CA A:Phe43 4.48 Na NE2 A:His44 3.84 Na CD2 A:His44 3.64 Na CG A:His44 4.86 Na OE1 A:Glu48 4.49 Na OD2 A:Asp83 4.31 Na NE2 A:Gln132 4.21 Na OE1 A:Gln132 2.64 Na CD A:Gln132 3.61 Na CG A:Gln132 4.68 Na O A:Hoh306 2.52 Na O A:Hoh308 4.13 interactive model: Sodium binding site 2 out of 5 in 1muq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1muq. 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: Leu13, B: Tyr15, B: Ala41, B: Ser42, B: Phe43, B: His44, B: Glu48, B: Asp83, B: Gln132, B: Hoh321, B: Hoh329, conact list: Atom Atom Distance (A) Na CD1 B:Leu13 3.87 Na CE2 B:Tyr15 3.76 Na CZ B:Tyr15 3.49 Na CE1 B:Tyr15 4.73 Na OH B:Tyr15 2.38 Na C B:Ala41 4.77 Na O B:Ser42 2.34 Na N B:Ser42 3.60 Na CB B:Ser42 3.91 Na OG B:Ser42 2.90 Na C B:Ser42 3.25 Na CA B:Ser42 3.83 Na N B:Phe43 4.28 Na CA B:Phe43 4.66 Na NE2 B:His44 4.38 Na CD2 B:His44 4.11 Na OE2 B:Glu48 4.94 Na OD2 B:Asp83 4.39 Na NE2 B:Gln132 3.91 Na OE1 B:Gln132 2.41 Na CD B:Gln132 3.30 Na CG B:Gln132 4.32 Na O B:Hoh321 3.22 Na O B:Hoh329 3.98 interactive model: Sodium binding site 3 out of 5 in 1muq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1muq. 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: Leu13, C: Tyr15, C: Ala41, C: Ser42, C: Phe43, C: His44, C: Glu48, C: Asp83, C: Gln132, C: Hoh311, conact list: Atom Atom Distance (A) Na CD1 C:Leu13 3.48 Na CG C:Leu13 4.85 Na CE2 C:Tyr15 3.68 Na CZ C:Tyr15 3.43 Na CE1 C:Tyr15 4.68 Na OH C:Tyr15 2.35 Na C C:Ala41 4.88 Na O C:Ser42 2.59 Na N C:Ser42 3.71 Na CB C:Ser42 3.91 Na OG C:Ser42 2.82 Na C C:Ser42 3.45 Na CA C:Ser42 3.94 Na N C:Phe43 4.47 Na CA C:Phe43 4.87 Na NE2 C:His44 4.43 Na CD2 C:His44 4.15 Na OE1 C:Glu48 4.90 Na OE2 C:Glu48 4.92 Na OD2 C:Asp83 4.33 Na NE2 C:Gln132 3.96 Na OE1 C:Gln132 2.23 Na CD C:Gln132 3.21 Na CG C:Gln132 4.17 Na O C:Hoh311 2.47 interactive model: Sodium binding site 4 out of 5 in 1muq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1muq. 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: Leu13, D: Tyr15, D: Ala41, D: Ser42, D: Phe43, D: His44, D: Asp83, D: Gln132, D: Hoh222, conact list: Atom Atom Distance (A) Na CD1 D:Leu13 3.61 Na CG D:Leu13 4.91 Na CE2 D:Tyr15 3.74 Na CZ D:Tyr15 3.61 Na CE1 D:Tyr15 4.88 Na OH D:Tyr15 2.62 Na C D:Ala41 4.73 Na O D:Ser42 2.37 Na N D:Ser42 3.51 Na CB D:Ser42 3.63 Na OG D:Ser42 2.55 Na C D:Ser42 3.26 Na CA D:Ser42 3.68 Na N D:Phe43 4.39 Na CA D:Phe43 4.86 Na NE2 D:His44 4.10 Na CD2 D:His44 4.12 Na OD2 D:Asp83 4.39 Na NE2 D:Gln132 3.67 Na OE1 D:Gln132 2.20 Na CD D:Gln132 3.10 Na CG D:Gln132 4.20 Na O D:Hoh222 4.34 interactive model: Sodium binding site 5 out of 5 in 1muq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1muq. 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: E: Leu13, E: Tyr15, E: Ala41, E: Ser42, E: Phe43, E: His44, E: Glu48, E: Asp83, E: Gln132, E: Hoh313, E: Hoh314, E: Hoh326, conact list: Atom Atom Distance (A) Na CD1 E:Leu13 3.67 Na CE2 E:Tyr15 3.66 Na CZ E:Tyr15 3.46 Na CE1 E:Tyr15 4.72 Na OH E:Tyr15 2.43 Na C E:Ala41 4.71 Na O E:Ser42 2.38 Na N E:Ser42 3.53 Na CB E:Ser42 3.75 Na OG E:Ser42 2.70 Na C E:Ser42 3.23 Na CA E:Ser42 3.76 Na N E:Phe43 4.25 Na CA E:Phe43 4.65 Na NE2 E:His44 4.52 Na CD2 E:His44 4.15 Na OE1 E:Glu48 4.82 Na OD2 E:Asp83 4.32 Na NE2 E:Gln132 3.92 Na OE1 E:Gln132 2.14 Na CB E:Gln132 4.95 Na CD E:Gln132 3.16 Na CG E:Gln132 4.14 Na O E:Hoh313 4.18 Na O E:Hoh314 2.22 Na O E:Hoh326 4.51 interactive model: