Calcium in the structure of Structure of the FAMILY43 Beta-Xylosidase From Geobacillus Stearothermophilus (pdb 2exh)

The binding sites of Calcium atom in the structure of Structure of the FAMILY43 Beta-Xylosidase From Geobacillus Stearothermophilus (pdb code 2exh). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 2exh structure was solved by C.BRUX, K.NIEFIND, D.SHALLOM-SHEZIFI, S.YUVAL, D.SCHOMBURG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-1.9 Space group P43212 a (A) 140.027 b (A) 140.027 c (A) 231.599 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.3 Rfree (%) 28.6 Calcium Binding Sites: Calcium binding site 1 out of 4 in 2exh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 2exh. 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: Hoh2125, A: Hoh2139, A: Hoh2202, A: Hoh2284, conact list: Atom Atom Distance (A) Ca O A:Asp333 2.43 Ca CB A:Asp333 3.71 Ca OD2 A:Asp333 4.51 Ca C A:Asp333 3.45 Ca OD1 A:Asp333 2.46 Ca CG A:Asp333 3.41 Ca CA A:Asp333 3.87 Ca N A:Phe334 4.61 Ca CB A:Phe334 4.85 Ca OD1 A:Asp335 4.92 Ca O A:Gly362 2.22 Ca C A:Gly362 3.29 Ca CA A:Gly362 3.77 Ca N A:His363 4.46 Ca ND1 A:His363 4.89 Ca CE1 A:His363 4.96 Ca CA A:His363 4.88 Ca O A:Asp528 2.41 Ca CB A:Asp528 4.36 Ca OD2 A:Asp528 2.35 Ca C A:Asp528 3.48 Ca OD1 A:Asp528 4.30 Ca CG A:Asp528 3.49 Ca CA A:Asp528 4.01 Ca N A:Tyr529 4.59 Ca CA A:Tyr529 4.98 Ca O A:Hoh2125 2.48 Ca O A:Hoh2139 2.48 Ca O A:Hoh2202 4.55 Ca O A:Hoh2284 4.76 interactive model: Calcium binding site 2 out of 4 in 2exh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 2exh. 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: Hoh2113, B: Hoh2162, B: Hoh2308, B: Hoh2398, conact list: Atom Atom Distance (A) Ca O B:Asp333 2.38 Ca CB B:Asp333 3.92 Ca C B:Asp333 3.39 Ca OD1 B:Asp333 4.35 Ca CG B:Asp333 4.56 Ca CA B:Asp333 3.83 Ca N B:Phe334 4.55 Ca CB B:Phe334 4.76 Ca OD1 B:Asp335 4.57 Ca O B:Gly362 2.29 Ca C B:Gly362 3.37 Ca CA B:Gly362 3.85 Ca N B:His363 4.54 Ca ND1 B:His363 4.94 Ca CA B:His363 4.96 Ca O B:Asp528 2.36 Ca CB B:Asp528 4.28 Ca OD2 B:Asp528 2.31 Ca C B:Asp528 3.40 Ca OD1 B:Asp528 4.36 Ca CG B:Asp528 3.47 Ca CA B:Asp528 3.94 Ca N B:Tyr529 4.51 Ca CB B:Tyr529 4.89 Ca CA B:Tyr529 4.89 Ca O B:Hoh2113 2.61 Ca O B:Hoh2162 2.63 Ca O B:Hoh2308 2.16 Ca O B:Hoh2398 4.93 interactive model: Calcium binding site 3 out of 4 in 2exh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 2exh. 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: Hoh2085, C: Hoh2101, C: Hoh2113, C: Hoh2143, conact list: Atom Atom Distance (A) Ca O C:Asp333 2.42 Ca CB C:Asp333 3.76 Ca OD2 C:Asp333 4.34 Ca C C:Asp333 3.38 Ca CG C:Asp333 4.59 Ca CA C:Asp333 3.72 Ca N C:Phe334 4.60 Ca CB C:Phe334 4.89 Ca OD1 C:Asp335 4.77 Ca O C:Gly362 2.70 Ca C C:Gly362 3.33 Ca CA C:Gly362 3.63 Ca N C:His363 4.35 Ca CA C:His363 4.94 Ca O C:Asp528 2.32 Ca CB C:Asp528 4.44 Ca OD2 C:Asp528 4.12 Ca C C:Asp528 3.34 Ca OD1 C:Asp528 3.80 Ca CG C:Asp528 3.88 Ca CA C:Asp528 3.93 Ca N C:Tyr529 4.42 Ca CB C:Tyr529 4.77 Ca CA C:Tyr529 4.77 Ca O C:Hoh2085 3.82 Ca O C:Hoh2101 2.57 Ca O C:Hoh2113 2.44 Ca O C:Hoh2143 3.14 interactive model: Calcium binding site 4 out of 4 in 2exh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 2exh. 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: Hoh2138, D: Hoh2343, D: Hoh2393, D: Hoh2400, conact list: Atom Atom Distance (A) Ca O D:Asp333 2.21 Ca CB D:Asp333 3.80 Ca OD2 D:Asp333 4.89 Ca C D:Asp333 3.26 Ca OD1 D:Asp333 2.78 Ca CG D:Asp333 3.70 Ca CA D:Asp333 3.77 Ca N D:Phe334 4.39 Ca CB D:Phe334 4.63 Ca C D:Phe334 4.95 Ca CA D:Phe334 4.84 Ca OD2 D:Asp335 4.98 Ca OD1 D:Asp335 4.40 Ca CG D:Asp335 4.97 Ca O D:Gly362 2.29 Ca C D:Gly362 3.34 Ca CA D:Gly362 3.77 Ca N D:His363 4.53 Ca CA D:His363 4.98 Ca O D:Asp528 2.35 Ca CB D:Asp528 4.16 Ca OD2 D:Asp528 4.06 Ca C D:Asp528 3.36 Ca OD1 D:Asp528 2.14 Ca CG D:Asp528 3.26 Ca CA D:Asp528 3.86 Ca N D:Tyr529 4.48 Ca CB D:Tyr529 4.91 Ca CA D:Tyr529 4.89 Ca O D:Hoh2138 2.79 Ca O D:Hoh2343 4.19 Ca O D:Hoh2393 3.17 Ca O D:Hoh2400 4.47 interactive model: