Magnesium in the structure of Complex of Fe-Type Nitrile Hydratase With Tert- Butylisonitrile, Photo-Activated For 18MIN At 293K (pdb 2zpf)

The binding sites of Magnesium atom in the structure of Complex of Fe-Type Nitrile Hydratase With Tert- Butylisonitrile, Photo-Activated For 18MIN At 293K (pdb code 2zpf). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2zpf structure was solved by K.HASHIMOTO, H.SUZUKI, K.TANIGUCHI, T.NOGUCHI, M.YOHDA, M.ODAKA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-1.5 Space group C121 a (A) 114.045 b (A) 59.995 c (A) 81.710 alpha (°) 90.00 beta (°) 125.06 gamma (°) 90.00 Rfactor (%) 16.8 Rfree (%) 19 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 2zpf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2zpf. 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: Arg174, A: Glu179, A: Hoh1604, A: Hoh1605, A: Hoh1606, A: Hoh1607, A: Hoh1608, A: Hoh1609, A: Hoh1674, A: Hoh1684, A: Hoh1737, A: Hoh1850, A: Hoh1875, conact list: Atom Atom Distance (A) Mg CD A:Arg174 4.92 Mg NH1 A:Arg174 4.78 Mg CG A:Glu179 4.87 Mg O A:Hoh1604 2.17 Mg O A:Hoh1605 2.18 Mg O A:Hoh1606 2.18 Mg O A:Hoh1607 2.17 Mg O A:Hoh1608 2.18 Mg O A:Hoh1609 2.17 Mg O A:Hoh1674 4.11 Mg O A:Hoh1684 4.16 Mg O A:Hoh1737 4.21 Mg O A:Hoh1850 4.49 Mg O A:Hoh1875 4.49 interactive model: Magnesium binding site 2 out of 4 in 2zpf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2zpf. 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: Gly180, A: Ser182, A: Gln185, A: Hoh1610, A: Hoh1611, A: Hoh1612, A: Hoh1613, A: Hoh1614, A: Hoh1615, A: Hoh1676, A: Hoh1872, conact list: Atom Atom Distance (A) Mg O A:Gly180 3.88 Mg C A:Gly180 4.83 Mg N A:Ser182 4.91 Mg NE2 A:Gln185 4.66 Mg OE1 A:Gln185 4.11 Mg CD A:Gln185 4.81 Mg O A:Hoh1610 2.18 Mg O A:Hoh1611 2.18 Mg O A:Hoh1612 2.18 Mg O A:Hoh1613 2.18 Mg O A:Hoh1614 2.18 Mg O A:Hoh1615 2.17 Mg O A:Hoh1676 4.27 Mg O A:Hoh1872 4.63 interactive model: Magnesium binding site 3 out of 4 in 2zpf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2zpf. 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: B: Asp2, B: Gly3, B: Asp6, B: Ala144, B: Hoh1606, B: Hoh1607, B: Hoh1608, B: Hoh1609, B: Hoh1610, B: Hoh1611, B: Hoh1664, B: Hoh1870, conact list: Atom Atom Distance (A) Mg O B:Asp2 4.47 Mg CB B:Asp2 4.55 Mg C B:Asp2 4.64 Mg OD1 B:Asp2 4.64 Mg CG B:Asp2 4.69 Mg CA B:Asp2 4.72 Mg O B:Gly3 4.49 Mg O B:Asp6 4.39 Mg CB B:Asp6 4.46 Mg OD2 B:Asp6 4.41 Mg CG B:Asp6 4.63 Mg CB B:Ala144 4.42 Mg O B:Hoh1606 2.17 Mg O B:Hoh1607 2.17 Mg O B:Hoh1608 2.15 Mg O B:Hoh1609 2.19 Mg O B:Hoh1610 2.17 Mg O B:Hoh1611 2.16 Mg O B:Hoh1664 4.29 Mg O B:Hoh1870 4.20 interactive model: Magnesium binding site 4 out of 4 in 2zpf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2zpf. 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: B: Met69, B: Pro71, B: Glu74, A: Hoh1664, A: Hoh1801, B: Hoh1612, B: Hoh1613, B: Hoh1614, B: Hoh1615, B: Hoh1616, B: Hoh1617, B: Hoh1638, B: Hoh1739, B: Hoh1781, conact list: Atom Atom Distance (A) Mg O B:Met69 4.57 Mg CE B:Met69 4.59 Mg CE B:Met69 4.49 Mg CD B:Pro71 4.55 Mg OE1 B:Glu74 4.37 Mg O A:Hoh1664 4.34 Mg O A:Hoh1801 4.21 Mg O B:Hoh1612 2.17 Mg O B:Hoh1613 2.18 Mg O B:Hoh1614 2.18 Mg O B:Hoh1615 2.17 Mg O B:Hoh1616 2.18 Mg O B:Hoh1617 2.17 Mg O B:Hoh1638 4.24 Mg O B:Hoh1739 4.38 Mg O B:Hoh1781 3.86 interactive model: