Magnesium in the structure of H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed With Dna (pdb 2o6m)

The binding sites of Magnesium atom in the structure of H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed With Dna (pdb code 2o6m). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2o6m structure was solved by J.H.EASTBERG, B.L.STODDARD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 49.3-2.3 Space group P3121 a (A) 113.850 b (A) 113.850 c (A) 88.880 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 21.1 Rfree (%) 24.4 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 2o6m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2o6m. 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: Ser297, B: Gln298, B: His301, B: Asn319, B: Asn323, C: Da413, C: Dg414, B: Hoh701, B: Hoh702, B: Hoh703, C: Hoh827, conact list: Atom Atom Distance (A) Mg OG B:Ser297 4.35 Mg C B:Ser297 4.65 Mg CA B:Ser297 4.61 Mg O B:Gln298 4.05 Mg N B:Gln298 3.84 Mg CB B:Gln298 4.52 Mg C B:Gln298 4.59 Mg CA B:Gln298 4.51 Mg ND1 B:His301 4.73 Mg CE1 B:His301 4.83 Mg O B:Asn319 3.84 Mg CB B:Asn319 4.63 Mg ND2 B:Asn319 3.97 Mg C B:Asn319 4.31 Mg OD1 B:Asn319 2.28 Mg CG B:Asn319 3.40 Mg CA B:Asn319 4.74 Mg OD1 B:Asn323 4.55 Mg C3' C:Da413 3.74 Mg O3' C:Da413 2.51 Mg C5' C:Da413 4.91 Mg C2' C:Da413 4.71 Mg C4' C:Da413 4.06 Mg OP1 C:Dg414 2.42 Mg P C:Dg414 3.01 Mg OP2 C:Dg414 4.09 Mg O5' C:Dg414 4.13 Mg O B:Hoh701 2.29 Mg O B:Hoh702 2.37 Mg O B:Hoh703 2.46 Mg O C:Hoh827 4.28 interactive model: Magnesium binding site 2 out of 2 in 2o6m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2o6m. 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: Ser97, A: Gln98, A: His101, A: Asn119, A: Lys120, A: Asn123, D: Da513, D: Dg514, A: Hoh704, A: Hoh705, A: Hoh706, D: Hoh934, conact list: Atom Atom Distance (A) Mg OG A:Ser97 4.30 Mg C A:Ser97 4.65 Mg CA A:Ser97 4.62 Mg O A:Gln98 4.09 Mg N A:Gln98 3.95 Mg CB A:Gln98 4.44 Mg C A:Gln98 4.67 Mg CA A:Gln98 4.57 Mg ND1 A:His101 4.76 Mg CE1 A:His101 4.86 Mg O A:Asn119 3.75 Mg CB A:Asn119 4.64 Mg ND2 A:Asn119 3.95 Mg C A:Asn119 4.26 Mg OD1 A:Asn119 2.26 Mg CG A:Asn119 3.39 Mg CA A:Asn119 4.78 Mg N A:Lys120 4.92 Mg OD1 A:Asn123 4.39 Mg C3' D:Da513 3.61 Mg O3' D:Da513 2.39 Mg C5' D:Da513 4.71 Mg C2' D:Da513 4.60 Mg C4' D:Da513 3.92 Mg OP1 D:Dg514 2.36 Mg P D:Dg514 2.93 Mg OP2 D:Dg514 4.02 Mg O5' D:Dg514 4.05 Mg O A:Hoh704 2.43 Mg O A:Hoh705 2.46 Mg O A:Hoh706 2.17 Mg O D:Hoh934 4.49 interactive model: