Magnesium in the structure of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria (pdb 2cw6)

The binding sites of Magnesium atom in the structure of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria (pdb code 2cw6). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2cw6 structure was solved by Z.FU, J.A.RUNQUIST, J.F.HUNT, H.M.MIZIORKO, J.-J.P.KIM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.4-2.1 Space group C121 a (A) 196.990 b (A) 117.080 c (A) 86.830 alpha (°) 90.00 beta (°) 112.50 gamma (°) 90.00 Rfactor (%) 22.6 Rfree (%) 26.5 Magnesium Binding Sites: Magnesium binding site 1 out of 6 in 2cw6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2cw6. 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: Asp42, A: His233, A: His235, A: Asn275, A: Hoh763, A: Hoh920, conact list: Atom Atom Distance (A) Mg CB A:Asp42 4.40 Mg OD2 A:Asp42 3.29 Mg OD1 A:Asp42 2.06 Mg CG A:Asp42 3.02 Mg NE2 A:His233 2.48 Mg ND1 A:His233 4.51 Mg CD2 A:His233 3.50 Mg CE1 A:His233 3.35 Mg CG A:His233 4.60 Mg NE2 A:His235 2.05 Mg ND1 A:His235 4.11 Mg CD2 A:His235 3.04 Mg CE1 A:His235 3.01 Mg CG A:His235 4.16 Mg CB A:Asn275 4.59 Mg ND2 A:Asn275 3.63 Mg OD1 A:Asn275 2.27 Mg CG A:Asn275 3.25 Mg CA A:Asn275 4.95 Mg O A:Hoh763 2.60 Mg O A:Hoh920 2.83 interactive model: Magnesium binding site 2 out of 6 in 2cw6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2cw6. 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: Asp42, B: His233, B: His235, B: Asn275, B: Hoh712, B: Hoh938, conact list: Atom Atom Distance (A) Mg CB B:Asp42 4.52 Mg OD2 B:Asp42 3.27 Mg OD1 B:Asp42 2.25 Mg CG B:Asp42 3.11 Mg NE2 B:His233 2.39 Mg ND1 B:His233 4.33 Mg CD2 B:His233 3.42 Mg CE1 B:His233 3.19 Mg CG B:His233 4.47 Mg NE2 B:His235 2.20 Mg ND1 B:His235 4.13 Mg CD2 B:His235 3.20 Mg CE1 B:His235 3.02 Mg CG B:His235 4.24 Mg CB B:Asn275 4.78 Mg ND2 B:Asn275 3.73 Mg OD1 B:Asn275 2.45 Mg CG B:Asn275 3.42 Mg O B:Hoh712 2.57 Mg O B:Hoh938 2.40 interactive model: Magnesium binding site 3 out of 6 in 2cw6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2cw6. 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: C: Asp42, C: His233, C: His235, C: Asn275, C: Hoh839, C: Hoh898, conact list: Atom Atom Distance (A) Mg CB C:Asp42 4.52 Mg OD2 C:Asp42 3.33 Mg OD1 C:Asp42 2.21 Mg CG C:Asp42 3.12 Mg NE2 C:His233 2.33 Mg ND1 C:His233 4.22 Mg CD2 C:His233 3.51 Mg CE1 C:His233 3.00 Mg CG C:His233 4.49 Mg NE2 C:His235 2.23 Mg ND1 C:His235 4.15 Mg CD2 C:His235 3.24 Mg CE1 C:His235 3.04 Mg CG C:His235 4.27 Mg CB C:Asn275 4.60 Mg ND2 C:Asn275 3.30 Mg OD1 C:Asn275 2.42 Mg CG C:Asn275 3.18 Mg O C:Hoh839 4.24 Mg O C:Hoh898 2.34 interactive model: Magnesium binding site 4 out of 6 in 2cw6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2cw6. 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: D: Asp42, D: His233, D: His235, D: Asn275, D: Hoh777, conact list: Atom Atom Distance (A) Mg CB D:Asp42 4.61 Mg OD2 D:Asp42 3.59 Mg OD1 D:Asp42 2.42 Mg CG D:Asp42 3.31 Mg NE2 D:His233 2.30 Mg ND1 D:His233 4.20 Mg CD2 D:His233 3.32 Mg CE1 D:His233 3.07 Mg CG D:His233 4.34 Mg NE2 D:His235 2.26 Mg ND1 D:His235 4.13 Mg CD2 D:His235 3.29 Mg CE1 D:His235 3.02 Mg CG D:His235 4.30 Mg CB D:Asn275 4.88 Mg ND2 D:Asn275 4.11 Mg OD1 D:Asn275 2.48 Mg CG D:Asn275 3.60 Mg O D:Hoh777 2.42 interactive model: Magnesium binding site 5 out of 6 in 2cw6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 2cw6. 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: E: Asp42, E: His233, E: His235, E: Asn275, E: Hoh860, conact list: Atom Atom Distance (A) Mg CB E:Asp42 4.49 Mg OD2 E:Asp42 3.34 Mg OD1 E:Asp42 2.16 Mg CG E:Asp42 3.10 Mg NE2 E:His233 2.51 Mg ND1 E:His233 4.26 Mg CD2 E:His233 3.57 Mg CE1 E:His233 3.13 Mg CG E:His233 4.51 Mg NE2 E:His235 2.26 Mg ND1 E:His235 4.28 Mg CD2 E:His235 3.30 Mg CE1 E:His235 3.12 Mg CG E:His235 4.39 Mg CB E:Asn275 4.83 Mg ND2 E:Asn275 3.75 Mg OD1 E:Asn275 2.51 Mg CG E:Asn275 3.46 Mg O E:Hoh860 2.44 interactive model: Magnesium binding site 6 out of 6 in 2cw6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 2cw6. 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: F: Asp42, F: His233, F: His235, F: Asn275, conact list: Atom Atom Distance (A) Mg CB F:Asp42 4.36 Mg OD2 F:Asp42 2.93 Mg OD1 F:Asp42 2.17 Mg CG F:Asp42 2.89 Mg NE2 F:His233 2.36 Mg ND1 F:His233 4.40 Mg CD2 F:His233 3.35 Mg CE1 F:His233 3.27 Mg CG F:His233 4.47 Mg NE2 F:His235 2.43 Mg ND1 F:His235 4.45 Mg CD2 F:His235 3.49 Mg CE1 F:His235 3.28 Mg CG F:His235 4.58 Mg CB F:Asn275 4.95 Mg ND2 F:Asn275 4.12 Mg OD1 F:Asn275 2.61 Mg CG F:Asn275 3.67 interactive model: