Sodium in the structure of Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex (pdb 2osx)

The binding sites of Sodium atom in the structure of Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex (pdb code 2osx). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2osx 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) 46.2-1.1 Space group C121 a (A) 77.801 b (A) 61.984 c (A) 102.846 alpha (°) 90.00 beta (°) 112.25 gamma (°) 90.00 Rfactor (%) 12.1 Rfree (%) 13.9 Sodium Binding Sites: Sodium binding site 1 out of 4 in 2osx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2osx. 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: Hoh680, A: Hoh696, A: Hoh717, A: Hoh745, A: Hoh758, A: Hoh777, A: Hoh779, A: Hoh856, A: Hoh1086, A: Hoh1150, conact list: Atom Atom Distance (A) Na O A:Phe219 4.44 Na O A:Ala220 4.28 Na O A:Asn222 2.38 Na N A:Asn222 4.41 Na CB A:Asn222 4.99 Na C A:Asn222 3.46 Na CA A:Asn222 4.47 Na O A:Asp223 4.76 Na N A:Asp223 4.21 Na C A:Asp223 4.34 Na CA A:Asp223 4.09 Na N A:Ala224 4.69 Na C A:Ala224 4.89 Na O A:Val225 2.31 Na N A:Val225 3.94 Na CB A:Val225 4.17 Na C A:Val225 3.44 Na CG1 A:Val225 4.85 Na CA A:Val225 4.04 Na N A:Val226 4.56 Na CA A:Val226 4.87 Na OG1 A:Thr267 4.27 Na O A:Hoh680 4.27 Na O A:Hoh696 2.30 Na O A:Hoh717 2.46 Na O A:Hoh745 2.40 Na O A:Hoh745 3.19 Na O A:Hoh758 2.43 Na O A:Hoh777 4.83 Na O A:Hoh777 4.64 Na O A:Hoh779 4.53 Na O A:Hoh856 4.24 Na O A:Hoh1086 4.70 Na O A:Hoh1150 3.78 interactive model: Sodium binding site 2 out of 4 in 2osx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2osx. 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: Hoh750, A: Hoh797, A: Hoh923, A: Hoh979, A: Hoh1034, A: Hoh1049, A: Hoh1154, A: Hoh1178, A: Hoh1179, conact list: Atom Atom Distance (A) Na O A:Ala162 2.41 Na C A:Ala162 3.51 Na CB A:Ala162 4.59 Na CA A:Ala162 4.31 Na N A:Trp163 4.41 Na C A:Trp163 4.62 Na CA A:Trp163 4.48 Na O A:Trp163 4.85 Na O A:Thr165 2.46 Na N A:Thr165 4.06 Na CB A:Thr165 3.98 Na CG2 A:Thr165 4.75 Na C A:Thr165 3.55 Na CA A:Thr165 4.07 Na N A:Tyr166 4.71 Na O A:Hoh750 3.78 Na O A:Hoh797 2.32 Na O A:Hoh797 2.53 Na O A:Hoh923 2.10 Na O A:Hoh979 2.45 Na O A:Hoh1034 4.05 Na O A:Hoh1049 4.74 Na O A:Hoh1154 4.59 Na O A:Hoh1178 4.49 Na O A:Hoh1179 3.38 interactive model: Sodium binding site 3 out of 4 in 2osx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2osx. 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: Asp290, A: Asp291, A: Pro292, A: Arg293, A: Gly295, A: Gln297, A: Hoh676, A: Hoh847, A: Hoh925, A: Hoh976, A: Hoh988, A: Hoh998, A: Hoh1008, conact list: Atom Atom Distance (A) Na C A:Asp290 4.99 Na O A:Asp291 2.30 Na N A:Asp291 3.91 Na CB A:Asp291 4.21 Na C A:Asp291 3.42 Na CA A:Asp291 4.08 Na N A:Pro292 4.48 Na C A:Pro292 4.97 Na CA A:Pro292 4.68 Na O A:Arg293 4.34 Na O A:Gly295 4.72 Na NE2 A:Gln297 4.72 Na OE1 A:Gln297 2.60 Na CB A:Gln297 4.78 Na CD A:Gln297 3.46 Na CG A:Gln297 3.61 Na CA A:Gln297 4.99 Na O A:Hoh676 2.44 Na O A:Hoh847 2.39 Na O A:Hoh925 4.39 Na O A:Hoh976 2.31 Na O A:Hoh988 2.51 Na O A:Hoh998 4.06 Na O A:Hoh1008 4.65 interactive model: Sodium binding site 4 out of 4 in 2osx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2osx. 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: Pro69, A: Asp70, A: Gly71, A: Arg99, A: Ser100, A: Arg115, A: Hoh637, A: Hoh671, A: Hoh763, A: Hoh769, A: Hoh1053, A: Hoh1166, conact list: Atom Atom Distance (A) Na O A:Pro69 2.21 Na C A:Pro69 3.41 Na CA A:Pro69 4.39 Na N A:Asp70 4.25 Na C A:Asp70 4.63 Na CA A:Asp70 4.19 Na N A:Gly71 4.89 Na NH2 A:Arg99 4.00 Na OG A:Ser100 4.80 Na NH2 A:Arg115 4.60 Na O A:Hoh637 3.70 Na O A:Hoh671 2.52 Na O A:Hoh763 4.38 Na O A:Hoh769 4.08 Na O A:Hoh1053 2.38 Na O A:Hoh1053 3.59 Na O A:Hoh1166 1.50 Na O A:Hoh1166 2.46 interactive model: