Magnesium in the structure of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum (pdb 3k1u)

The binding sites of Magnesium atom in the structure of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum (pdb code 3k1u). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3k1u structure was solved by J.OSIPIUK, R.WU, R.JEDRZEJCZAK, A.JOACHIMIAK, MIDWEST CENTER FORSTRUCTURAL GENOMICS (MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 37.2-1.6 Space group P212121 a (A) 47.450 b (A) 59.658 c (A) 112.391 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 13.6 Rfree (%) 16.1 Magnesium Binding Sites: Magnesium binding site 1 out of 3 in 3k1u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3k1u. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ala73, A: Glu75, A: Asp135, A: Ala136, A: Thr137, A: Gly197, A: Pro198, A: His260, A: Asn261, A: Hoh352, A: Hoh358, A: Hoh369, A: Hoh372, A: Hoh424, A: Hoh427, A: Hoh512, A: Hoh560, conact list: Atom Atom Distance (A) Mg O A:Ala73 4.91 Mg OE1 A:Glu75 4.21 Mg OE2 A:Glu75 2.07 Mg CD A:Glu75 3.13 Mg CG A:Glu75 3.60 Mg O A:Asp135 4.36 Mg CB A:Asp135 4.97 Mg C A:Asp135 4.84 Mg CA A:Asp135 4.97 Mg O A:Ala136 4.66 Mg CB A:Thr137 4.94 Mg C A:Gly197 4.93 Mg CA A:Gly197 4.92 Mg O A:Pro198 3.86 Mg NE2 A:His260 2.26 Mg ND1 A:His260 4.38 Mg CD2 A:His260 3.21 Mg CE1 A:His260 3.27 Mg CG A:His260 4.38 Mg O A:Asn261 4.56 Mg O A:Hoh352 3.95 Mg O A:Hoh358 4.48 Mg O A:Hoh369 2.15 Mg O A:Hoh372 4.09 Mg O A:Hoh424 2.12 Mg O A:Hoh427 4.04 Mg O A:Hoh512 2.06 Mg O A:Hoh560 2.12 interactive model: Magnesium binding site 2 out of 3 in 3k1u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3k1u. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp97, A: Asp98, A: Hoh441, A: Hoh450, A: Hoh470, A: Hoh504, A: Hoh576, A: Hoh591, A: Hoh627, A: Hoh642, A: Hoh665, conact list: Atom Atom Distance (A) Mg O A:Asp97 4.57 Mg CB A:Asp97 4.67 Mg C A:Asp97 4.64 Mg OD1 A:Asp97 4.32 Mg CG A:Asp97 4.97 Mg CA A:Asp97 4.41 Mg OD2 A:Asp98 3.84 Mg OD1 A:Asp98 4.09 Mg CG A:Asp98 4.24 Mg O A:Hoh441 2.12 Mg O A:Hoh450 2.22 Mg O A:Hoh470 2.15 Mg O A:Hoh504 1.94 Mg O A:Hoh576 2.04 Mg O A:Hoh591 3.96 Mg O A:Hoh627 4.54 Mg O A:Hoh642 4.54 Mg O A:Hoh665 2.19 interactive model: Magnesium binding site 3 out of 3 in 3k1u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3k1u. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Tyr20, A: Asn23, A: Phe78, A: Hoh536, A: Hoh561, A: Hoh595, A: Hoh604, A: Hoh646, A: Hoh647, A: Hoh648, A: Hoh649, A: Hoh650, conact list: Atom Atom Distance (A) Mg CZ A:Tyr20 4.87 Mg CE1 A:Tyr20 4.66 Mg OH A:Tyr20 4.12 Mg OD1 A:Asn23 4.40 Mg O A:Phe78 4.40 Mg O A:Hoh536 4.49 Mg O A:Hoh561 2.06 Mg O A:Hoh595 4.11 Mg O A:Hoh604 2.09 Mg O A:Hoh646 2.03 Mg O A:Hoh647 4.01 Mg O A:Hoh648 2.01 Mg O A:Hoh649 2.14 Mg O A:Hoh650 1.97 interactive model: