Magnesium in the structure of Topoisomerase VI-B, Adp-Bound Dimer Form (pdb 1z5a)

The binding sites of Magnesium atom in the structure of Topoisomerase VI-B, Adp-Bound Dimer Form (pdb code 1z5a). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1z5a structure was solved by K.D.CORBETT, J.M.BERGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.2 Space group P3212 a (A) 74.569 b (A) 74.569 c (A) 345.557 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.5 Rfree (%) 23.1 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 1z5a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1z5a. 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: Glu38, A: Asn42, A: Lys98, A: Gly106, A: Gly111, A: Val112, A: Adp2001, A: Hoh2024, A: Hoh2026, A: Hoh2060, A: Hoh2087, A: Hoh2088, conact list: Atom Atom Distance (A) Mg O A:Glu38 4.67 Mg OE2 A:Glu38 4.29 Mg CB A:Asn42 4.55 Mg ND2 A:Asn42 3.42 Mg OD1 A:Asn42 2.25 Mg CG A:Asn42 3.16 Mg CA A:Asn42 4.87 Mg NZ A:Lys98 3.87 Mg N A:Gly106 4.76 Mg CA A:Gly106 3.99 Mg CA A:Gly111 4.76 Mg N A:Val112 4.97 Mg O3B A:Adp2001 4.14 Mg PA A:Adp2001 3.07 Mg O2A A:Adp2001 2.23 Mg O1B A:Adp2001 1.75 Mg PB A:Adp2001 2.88 Mg O5' A:Adp2001 3.70 Mg O2B A:Adp2001 3.56 Mg O3A A:Adp2001 3.10 Mg O1A A:Adp2001 4.42 Mg O A:Hoh2024 4.63 Mg O A:Hoh2026 4.14 Mg O A:Hoh2060 2.61 Mg O A:Hoh2087 2.22 Mg O A:Hoh2088 2.19 interactive model: Magnesium binding site 2 out of 2 in 1z5a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1z5a. 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: Glu38, B: Asn42, B: Lys98, B: Gly106, B: Gly111, B: Val112, B: Adp2002, B: Hoh2003, B: Hoh2021, B: Hoh2056, B: Hoh2119, conact list: Atom Atom Distance (A) Mg O B:Glu38 4.49 Mg OE2 B:Glu38 4.31 Mg N B:Asn42 4.79 Mg CB B:Asn42 4.40 Mg ND2 B:Asn42 3.46 Mg OD1 B:Asn42 2.05 Mg CG B:Asn42 3.05 Mg CA B:Asn42 4.65 Mg CE B:Lys98 4.91 Mg NZ B:Lys98 3.61 Mg N B:Gly106 4.97 Mg CA B:Gly106 4.21 Mg CA B:Gly111 4.79 Mg N B:Val112 4.88 Mg O3B B:Adp2002 4.26 Mg PA B:Adp2002 3.17 Mg O2A B:Adp2002 2.19 Mg O1B B:Adp2002 1.83 Mg PB B:Adp2002 3.07 Mg O5' B:Adp2002 3.78 Mg O2B B:Adp2002 3.77 Mg O3A B:Adp2002 3.34 Mg O1A B:Adp2002 4.48 Mg O B:Hoh2003 5.00 Mg O B:Hoh2021 4.11 Mg O B:Hoh2056 2.22 Mg O B:Hoh2119 2.59 interactive model: