Magnesium in the structure of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex With Glcnac, Ethylene Glycol, and Nitrate (pdb 2zuv)

The binding sites of Magnesium atom in the structure of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex With Glcnac, Ethylene Glycol, and Nitrate (pdb code 2zuv). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2zuv structure was solved by M.HIDAKA, M.NISHIMOTO, M.KITAOKA, T.WAKAGI, H.SHOUN, S.FUSHINOBU, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 35.1-1.9 Space group C121 a (A) 204.043 b (A) 68.020 c (A) 116.047 alpha (°) 90.00 beta (°) 108.79 gamma (°) 90.00 Rfactor (%) 14.9 Rfree (%) 19.2 Magnesium Binding Sites: Magnesium binding site 1 out of 8 in 2zuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2zuv. 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: Asp79, A: Ser95, A: Glu224, A: Lys229, B: Glu640, A: Hoh771, A: Hoh931, A: Hoh985, A: Hoh1035, A: Hoh1477, A: Hoh1525, A: Hoh1621, A: Hoh1639, A: Hoh1658, B: Hoh1230, B: Hoh1234, B: Hoh1649, conact list: Atom Atom Distance (A) Mg OD2 A:Asp79 4.24 Mg OD1 A:Asp79 4.32 Mg CG A:Asp79 4.72 Mg CB A:Ser95 4.30 Mg CA A:Ser95 4.93 Mg OE1 A:Glu224 4.29 Mg OE2 A:Glu224 4.27 Mg CD A:Glu224 4.72 Mg NZ A:Lys229 4.43 Mg OE2 B:Glu640 4.46 Mg O A:Hoh771 4.04 Mg O A:Hoh931 4.32 Mg O A:Hoh985 2.15 Mg O A:Hoh1035 4.49 Mg O A:Hoh1477 4.87 Mg O A:Hoh1525 2.14 Mg O A:Hoh1621 2.27 Mg O A:Hoh1639 2.16 Mg O A:Hoh1658 2.10 Mg O B:Hoh1230 4.22 Mg O B:Hoh1234 4.04 Mg O B:Hoh1649 1.97 interactive model: Magnesium binding site 2 out of 8 in 2zuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2zuv. 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: Arg272, A: Asp511, B: Arg550, A: Hoh1221, A: Hoh1343, A: Hoh1423, A: Hoh1464, A: Hoh1466, A: Hoh1486, A: Hoh1529, A: Hoh1757, B: Hoh971, B: Hoh1461, conact list: Atom Atom Distance (A) Mg CZ A:Arg272 4.81 Mg NH2 A:Arg272 4.83 Mg NH1 A:Arg272 3.93 Mg OD2 A:Asp511 4.18 Mg CG B:Arg550 4.96 Mg NE B:Arg550 4.87 Mg O A:Hoh1221 4.42 Mg O A:Hoh1343 2.15 Mg O A:Hoh1423 3.95 Mg O A:Hoh1464 2.24 Mg O A:Hoh1466 2.12 Mg O A:Hoh1486 4.67 Mg O A:Hoh1529 2.15 Mg O A:Hoh1757 2.00 Mg O B:Hoh971 4.24 Mg O B:Hoh1461 4.19 interactive model: Magnesium binding site 3 out of 8 in 2zuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2zuv. 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: Lys48, A: Gln205, A: Asp207, A: Hoh1318, A: Hoh1489, A: Hoh1642, A: Hoh1784, conact list: Atom Atom Distance (A) Mg O A:Lys48 4.64 Mg O A:Gln205 4.52 Mg NE2 A:Gln205 4.36 Mg OD2 A:Asp207 4.18 Mg OD1 A:Asp207 4.22 Mg CG A:Asp207 4.63 Mg O A:Hoh1318 2.14 Mg O A:Hoh1489 4.05 Mg O A:Hoh1642 2.18 Mg O A:Hoh1784 4.30 interactive model: Magnesium binding site 4 out of 8 in 2zuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2zuv. 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: Asp79, B: Ser95, B: Glu224, B: Lys229, A: Hoh908, A: Hoh1132, A: Hoh1553, A: Hoh1661, A: Hoh1762, B: Hoh797, B: Hoh921, B: Hoh986, B: Hoh1227, B: Hoh1331, B: Hoh1358, B: Hoh1497, B: Hoh1512, B: Hoh1641, conact list: Atom Atom Distance (A) Mg OD2 B:Asp79 4.34 Mg OD1 B:Asp79 4.30 Mg CG B:Asp79 4.77 Mg CB B:Ser95 4.23 Mg CA B:Ser95 4.85 Mg OE1 B:Glu224 4.20 Mg OE2 B:Glu224 4.23 Mg CD B:Glu224 4.67 Mg NZ B:Lys229 4.10 Mg O A:Hoh908 3.98 Mg O A:Hoh1132 4.34 Mg O A:Hoh1553 4.89 Mg O A:Hoh1661 2.15 Mg O A:Hoh1762 4.88 Mg O B:Hoh797 2.21 Mg O B:Hoh921 4.01 Mg O B:Hoh986 2.10 Mg O B:Hoh1227 4.48 Mg O B:Hoh1331 2.17 Mg O B:Hoh1358 2.21 Mg O B:Hoh1497 4.61 Mg O B:Hoh1512 4.51 Mg O B:Hoh1641 2.12 interactive model: Magnesium binding site 5 out of 8 in 2zuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 2zuv. 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: Asp595, B: Hoh1589, B: Hoh1609, B: Hoh1640, B: Hoh1650, B: Hoh1696, conact list: Atom Atom Distance (A) Mg CB B:Asp595 4.31 Mg OD2 B:Asp595 2.16 Mg OD1 B:Asp595 3.54 Mg CG B:Asp595 3.12 Mg O B:Hoh1589 4.97 Mg O B:Hoh1609 2.13 Mg O B:Hoh1640 2.15 Mg O B:Hoh1650 2.10 Mg O B:Hoh1696 3.92 interactive model: Magnesium binding site 6 out of 8 in 2zuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 2zuv. 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: Glu135, B: Hoh1526, B: Hoh1553, conact list: Atom Atom Distance (A) Mg OE1 B:Glu135 4.32 Mg OE2 B:Glu135 4.25 Mg CD B:Glu135 4.73 Mg O B:Hoh1526 1.99 Mg O B:Hoh1553 4.63 interactive model: Magnesium binding site 7 out of 8 in 2zuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 2zuv. 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: Arg243, B: Asp246, B: Asp247, B: Hoh1056, B: Hoh1135, B: Hoh1660, conact list: Atom Atom Distance (A) Mg O B:Arg243 4.45 Mg CG B:Arg243 4.83 Mg CB B:Asp246 4.94 Mg N B:Asp247 4.63 Mg CB B:Asp247 4.55 Mg OD2 B:Asp247 3.67 Mg OD1 B:Asp247 2.21 Mg CG B:Asp247 3.27 Mg CA B:Asp247 4.71 Mg O B:Hoh1056 4.50 Mg O B:Hoh1135 1.93 Mg O B:Hoh1660 1.87 interactive model: Magnesium binding site 8 out of 8 in 2zuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 2zuv. 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: Arg550, B: Arg272, B: Asp511, A: Hoh866, A: Hoh1177, A: Hoh1687, B: Hoh799, B: Hoh973, B: Hoh1064, B: Hoh1306, B: Hoh1588, B: Hoh1688, B: Hoh1694, B: Hoh1705, conact list: Atom Atom Distance (A) Mg CD A:Arg550 4.39 Mg CZ B:Arg272 4.55 Mg NH2 B:Arg272 4.52 Mg NH1 B:Arg272 3.74 Mg OD2 B:Asp511 4.11 Mg O A:Hoh866 4.14 Mg O A:Hoh1177 4.15 Mg O A:Hoh1687 2.26 Mg O B:Hoh799 4.58 Mg O B:Hoh973 4.24 Mg O B:Hoh1064 4.24 Mg O B:Hoh1306 4.33 Mg O B:Hoh1588 4.94 Mg O B:Hoh1688 2.19 Mg O B:Hoh1694 2.12 Mg O B:Hoh1705 2.08 interactive model: