Sodium in the structure of Endo-Glycoceramidase II From Rhodococcus Sp. (pdb 2osw)

The binding sites of Sodium atom in the structure of Endo-Glycoceramidase II From Rhodococcus Sp. (pdb code 2osw). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2osw structure was solved by M.E.C.CAINES, N.C.J.STRYNADKA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.6-1.6 Space group P1211 a (A) 53.750 b (A) 92.941 c (A) 94.545 alpha (°) 90.00 beta (°) 98.55 gamma (°) 90.00 Rfactor (%) 18.1 Rfree (%) 20.4 Sodium Binding Sites: Sodium binding site 1 out of 4 in 2osw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2osw. 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: Phe219, A: Ala220, A: Asn222, A: Asp223, A: Ala224, A: Val225, A: Val226, A: Thr267, A: Hoh620, A: Hoh687, A: Hoh691, A: Hoh715, A: Hoh740, A: Hoh804, A: Hoh808, A: Hoh921, A: Hoh943, conact list: Atom Atom Distance (A) Na O A:Phe219 4.42 Na O A:Ala220 4.30 Na O A:Asn222 2.42 Na N A:Asn222 4.46 Na C A:Asn222 3.50 Na CA A:Asn222 4.51 Na O A:Asp223 4.49 Na N A:Asp223 4.25 Na C A:Asp223 4.29 Na CA A:Asp223 4.19 Na N A:Ala224 4.78 Na C A:Ala224 4.96 Na O A:Val225 2.31 Na N A:Val225 4.02 Na CB A:Val225 4.18 Na C A:Val225 3.46 Na CG1 A:Val225 4.78 Na CA A:Val225 4.08 Na N A:Val226 4.55 Na CA A:Val226 4.85 Na CA A:Val226 4.85 Na OG1 A:Thr267 4.17 Na O A:Hoh620 4.51 Na O A:Hoh687 2.43 Na O A:Hoh691 2.35 Na O A:Hoh715 2.41 Na O A:Hoh740 4.52 Na O A:Hoh804 4.74 Na O A:Hoh808 2.37 Na O A:Hoh921 4.12 Na O A:Hoh943 3.48 interactive model: Sodium binding site 2 out of 4 in 2osw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2osw. 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: Ala162, A: Trp163, A: Thr165, A: Tyr166, A: Hoh767, A: Hoh900, A: Hoh1062, A: Hoh1063, conact list: Atom Atom Distance (A) Na O A:Ala162 2.58 Na C A:Ala162 3.71 Na CA A:Ala162 4.67 Na N A:Trp163 4.51 Na C A:Trp163 4.47 Na CA A:Trp163 4.44 Na O A:Trp163 4.51 Na O A:Thr165 2.36 Na N A:Thr165 4.06 Na CB A:Thr165 4.15 Na CG2 A:Thr165 4.93 Na C A:Thr165 3.48 Na CA A:Thr165 4.10 Na N A:Tyr166 4.57 Na CA A:Tyr166 4.89 Na O A:Hoh767 4.07 Na O A:Hoh900 2.32 Na O A:Hoh1062 2.29 Na O A:Hoh1063 2.22 interactive model: Sodium binding site 3 out of 4 in 2osw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2osw. 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: Phe219, B: Ala220, B: Asn222, B: Asp223, B: Ala224, B: Val225, B: Val226, B: Thr267, B: Hoh683, B: Hoh763, B: Hoh766, B: Hoh779, B: Hoh845, B: Hoh851, B: Hoh937, B: Hoh969, conact list: Atom Atom Distance (A) Na O B:Phe219 4.37 Na O B:Ala220 4.16 Na C B:Ala220 4.94 Na O B:Asn222 2.46 Na N B:Asn222 4.45 Na C B:Asn222 3.52 Na CA B:Asn222 4.53 Na O B:Asp223 4.47 Na N B:Asp223 4.23 Na C B:Asp223 4.25 Na CA B:Asp223 4.09 Na N B:Ala224 4.75 Na C B:Ala224 4.99 Na O B:Val225 2.34 Na N B:Val225 4.05 Na CB B:Val225 4.17 Na C B:Val225 3.49 Na CG1 B:Val225 4.86 Na CA B:Val225 4.12 Na N B:Val226 4.59 Na CA B:Val226 4.88 Na OG1 B:Thr267 4.15 Na O B:Hoh683 4.49 Na O B:Hoh763 2.34 Na O B:Hoh766 2.32 Na O B:Hoh779 2.39 Na O B:Hoh845 2.31 Na O B:Hoh851 4.21 Na O B:Hoh937 4.29 Na O B:Hoh969 4.68 interactive model: Sodium binding site 4 out of 4 in 2osw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2osw. 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: Ala162, B: Trp163, B: Thr165, B: Tyr166, B: Hoh684, B: Hoh781, B: Hoh889, conact list: Atom Atom Distance (A) Na O B:Ala162 2.48 Na C B:Ala162 3.57 Na CB B:Ala162 4.77 Na CA B:Ala162 4.48 Na N B:Trp163 4.40 Na C B:Trp163 4.52 Na CA B:Trp163 4.40 Na O B:Trp163 4.61 Na O B:Thr165 2.45 Na N B:Thr165 4.14 Na CB B:Thr165 4.17 Na CG2 B:Thr165 4.98 Na C B:Thr165 3.57 Na CA B:Thr165 4.16 Na N B:Tyr166 4.69 Na O B:Hoh684 2.68 Na O B:Hoh781 3.99 Na O B:Hoh889 2.27 interactive model: