Calcium in the structure of Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex With Xylobiose (pdb 2exk)

The binding sites of Calcium atom in the structure of Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex With Xylobiose (pdb code 2exk). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 2exk structure was solved by C.BRUX, K.NIEFIND, D.SHALLOM-SHEZIFI, Y.SHOHAM, D.SCHOMBURG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 2.2-2.2 Space group P43212 a (A) 139.870 b (A) 139.870 c (A) 232.025 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.5 Rfree (%) 23.8 Calcium Binding Sites: Calcium binding site 1 out of 4 in 2exk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 2exk. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp333, A: Phe334, A: Asp335, A: Gly362, A: His363, A: Asp528, A: Tyr529, A: Hoh2054, A: Hoh2062, A: Hoh2294, A: Hoh2320, conact list: Atom Atom Distance (A) Ca O A:Asp333 2.46 Ca CB A:Asp333 3.88 Ca OD2 A:Asp333 4.87 Ca C A:Asp333 3.46 Ca OD1 A:Asp333 2.80 Ca CG A:Asp333 3.71 Ca CA A:Asp333 3.88 Ca O A:Phe334 4.97 Ca N A:Phe334 4.63 Ca CB A:Phe334 4.85 Ca OD1 A:Asp335 4.96 Ca O A:Gly362 2.24 Ca C A:Gly362 3.34 Ca CA A:Gly362 3.87 Ca N A:His363 4.48 Ca ND1 A:His363 4.76 Ca CE1 A:His363 4.89 Ca CA A:His363 4.85 Ca O A:Asp528 2.42 Ca CB A:Asp528 4.39 Ca OD2 A:Asp528 2.39 Ca C A:Asp528 3.49 Ca OD1 A:Asp528 4.32 Ca CG A:Asp528 3.52 Ca CA A:Asp528 4.02 Ca N A:Tyr529 4.61 Ca CB A:Tyr529 4.98 Ca CA A:Tyr529 4.96 Ca O A:Hoh2054 2.38 Ca O A:Hoh2062 2.67 Ca O A:Hoh2294 4.80 Ca O A:Hoh2320 4.35 interactive model: Calcium binding site 2 out of 4 in 2exk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 2exk. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp333, B: Phe334, B: Asp335, B: Gly362, B: His363, B: Asp528, B: Tyr529, B: Hoh2100, B: Hoh2255, B: Hoh2262, conact list: Atom Atom Distance (A) Ca O B:Asp333 2.44 Ca CB B:Asp333 4.01 Ca C B:Asp333 3.42 Ca OD1 B:Asp333 4.06 Ca CG B:Asp333 4.51 Ca CA B:Asp333 3.85 Ca N B:Phe334 4.57 Ca CB B:Phe334 4.78 Ca OD1 B:Asp335 4.47 Ca O B:Gly362 2.21 Ca C B:Gly362 3.32 Ca CA B:Gly362 3.85 Ca N B:His363 4.48 Ca ND1 B:His363 4.84 Ca CE1 B:His363 4.96 Ca CA B:His363 4.88 Ca O B:Asp528 2.41 Ca CB B:Asp528 4.22 Ca OD2 B:Asp528 2.22 Ca C B:Asp528 3.41 Ca OD1 B:Asp528 4.20 Ca CG B:Asp528 3.37 Ca CA B:Asp528 3.92 Ca N B:Tyr529 4.52 Ca CB B:Tyr529 4.81 Ca CA B:Tyr529 4.89 Ca O B:Hoh2100 2.63 Ca O B:Hoh2255 2.24 Ca O B:Hoh2262 2.65 interactive model: Calcium binding site 3 out of 4 in 2exk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 2exk. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asp333, C: Phe334, C: Asp335, C: Gly362, C: His363, C: Asp528, C: Tyr529, C: Hoh2080, C: Hoh2100, conact list: Atom Atom Distance (A) Ca O C:Asp333 2.63 Ca CB C:Asp333 3.76 Ca OD2 C:Asp333 2.89 Ca C C:Asp333 3.52 Ca OD1 C:Asp333 4.95 Ca CG C:Asp333 3.74 Ca CA C:Asp333 3.78 Ca N C:Phe334 4.72 Ca OD1 C:Asp335 4.56 Ca O C:Gly362 2.30 Ca C C:Gly362 3.39 Ca CA C:Gly362 3.93 Ca NE2 C:His363 4.90 Ca N C:His363 4.53 Ca CD2 C:His363 4.90 Ca CE1 C:His363 4.98 Ca CG C:His363 4.96 Ca CA C:His363 4.88 Ca O C:Asp528 2.52 Ca CB C:Asp528 4.23 Ca OD2 C:Asp528 3.12 Ca C C:Asp528 3.38 Ca OD1 C:Asp528 3.80 Ca CG C:Asp528 3.45 Ca CA C:Asp528 3.86 Ca N C:Tyr529 4.43 Ca CB C:Tyr529 4.85 Ca CA C:Tyr529 4.87 Ca O C:Hoh2080 2.75 Ca O C:Hoh2100 3.24 interactive model: Calcium binding site 4 out of 4 in 2exk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 2exk. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asp333, D: Phe334, D: Asp335, D: Gly362, D: His363, D: Asp528, D: Tyr529, D: Hoh2111, D: Hoh2263, conact list: Atom Atom Distance (A) Ca O D:Asp333 2.36 Ca CB D:Asp333 3.85 Ca C D:Asp333 3.37 Ca OD1 D:Asp333 2.93 Ca CG D:Asp333 3.81 Ca CA D:Asp333 3.84 Ca N D:Phe334 4.51 Ca CB D:Phe334 4.73 Ca CA D:Phe334 4.97 Ca OD1 D:Asp335 4.51 Ca O D:Gly362 2.24 Ca C D:Gly362 3.33 Ca CA D:Gly362 3.86 Ca NE2 D:His363 4.93 Ca N D:His363 4.48 Ca CD2 D:His363 4.93 Ca CG D:His363 5.00 Ca CA D:His363 4.86 Ca O D:Asp528 2.46 Ca CB D:Asp528 4.24 Ca OD2 D:Asp528 4.06 Ca C D:Asp528 3.46 Ca OD1 D:Asp528 2.30 Ca CG D:Asp528 3.33 Ca CA D:Asp528 3.95 Ca N D:Tyr529 4.57 Ca CB D:Tyr529 4.95 Ca CA D:Tyr529 4.94 Ca O D:Hoh2111 2.45 Ca O D:Hoh2263 3.58 interactive model: