Magnesium in the structure of Crystal Structure of PDE8A Catalytic Domain in Complex With Ibmx (pdb 3ecn)

The binding sites of Magnesium atom in the structure of Crystal Structure of PDE8A Catalytic Domain in Complex With Ibmx (pdb code 3ecn). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3ecn structure was solved by H.WANG, Z.YAN, S.YANG, J.CAI, H.ROBINSON, H.KE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.1 Space group P1211 a (A) 76.325 b (A) 101.601 c (A) 76.573 alpha (°) 90.00 beta (°) 119.90 gamma (°) 90.00 Rfactor (%) 22.1 Rfree (%) 25.6 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 3ecn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3ecn. 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: His556, A: His596, A: Asp597, A: His600, A: Glu626, A: His629, A: Thr668, A: Asp726, A: Zn1, A: Hoh820, A: Hoh821, A: Hoh822, A: Hoh823, A: Hoh824, A: Hoh825, A: Hoh826, A: Hoh842, conact list: Atom Atom Distance (A) Mg NE2 A:His556 4.90 Mg O A:His596 4.13 Mg NE2 A:His596 4.98 Mg CD2 A:His596 4.41 Mg C A:His596 4.99 Mg CB A:Asp597 4.63 Mg OD2 A:Asp597 3.71 Mg OD1 A:Asp597 2.28 Mg CG A:Asp597 3.33 Mg CA A:Asp597 4.85 Mg NE2 A:His600 4.83 Mg CD2 A:His600 4.44 Mg OE2 A:Glu626 3.83 Mg CD A:Glu626 4.67 Mg CG A:Glu626 4.80 Mg NE2 A:His629 4.04 Mg CD2 A:His629 4.24 Mg CB A:Thr668 4.66 Mg OG1 A:Thr668 4.11 Mg OD2 A:Asp726 4.62 Mg ZN A:Zn1 4.17 Mg O A:Hoh820 2.38 Mg O A:Hoh821 4.27 Mg O A:Hoh822 2.37 Mg O A:Hoh823 2.36 Mg O A:Hoh824 2.24 Mg O A:Hoh825 2.20 Mg O A:Hoh826 3.98 Mg O A:Hoh842 4.06 interactive model: Magnesium binding site 2 out of 2 in 3ecn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3ecn. 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: His596, B: Asp597, B: His600, B: Glu626, B: His629, B: Thr668, B: Asp726, B: Zn1, B: Hoh11, B: Hoh12, B: Hoh13, B: Hoh14, B: Hoh15, B: Hoh16, B: Hoh17, B: Hoh133, conact list: Atom Atom Distance (A) Mg O B:His596 4.07 Mg NE2 B:His596 4.90 Mg CD2 B:His596 4.30 Mg C B:His596 4.92 Mg CB B:Asp597 4.58 Mg OD2 B:Asp597 3.63 Mg OD1 B:Asp597 2.26 Mg CG B:Asp597 3.28 Mg CA B:Asp597 4.80 Mg NE2 B:His600 4.90 Mg CD2 B:His600 4.50 Mg OE2 B:Glu626 3.72 Mg CD B:Glu626 4.64 Mg CG B:Glu626 4.81 Mg NE2 B:His629 3.94 Mg CD2 B:His629 4.13 Mg O B:Thr668 4.95 Mg CB B:Thr668 4.61 Mg OG1 B:Thr668 4.02 Mg OD2 B:Asp726 4.60 Mg ZN B:Zn1 4.19 Mg O B:Hoh11 2.43 Mg O B:Hoh12 4.35 Mg O B:Hoh13 2.41 Mg O B:Hoh14 2.38 Mg O B:Hoh15 2.20 Mg O B:Hoh16 2.19 Mg O B:Hoh17 4.08 Mg O B:Hoh133 4.14 interactive model: