Magnesium in the structure of L1 Ribozyme Ligase Circular Adduct (pdb 2oiu)

The binding sites of Magnesium atom in the structure of L1 Ribozyme Ligase Circular Adduct (pdb code 2oiu). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2oiu structure was solved by M.P ROBERTSON, W.G.SCOTT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 31.3-2.6 Space group P1211 a (A) 45.290 b (A) 100.018 c (A) 71.930 alpha (°) 90.00 beta (°) 104.42 gamma (°) 90.00 Rfactor (%) 20.3 Rfree (%) 23.8 Magnesium Binding Sites: Magnesium binding site 1 out of 7 in 2oiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2oiu. 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: Q: G1, Q: U38, Q: A39, Q: G40, Q: U71, Q: Hoh93, conact list: Atom Atom Distance (A) Mg OP1 Q:G1 2.22 Mg P Q:G1 3.07 Mg OP2 Q:G1 4.01 Mg C5' Q:G1 4.41 Mg O5' Q:G1 4.30 Mg O3' Q:U38 4.69 Mg OP1 Q:A39 2.20 Mg C3' Q:A39 4.65 Mg P Q:A39 3.42 Mg O3' Q:A39 4.58 Mg OP2 Q:A39 3.91 Mg C5' Q:A39 4.68 Mg O5' Q:A39 3.99 Mg OP1 Q:G40 4.62 Mg C8 Q:G40 4.79 Mg P Q:G40 3.71 Mg N7 Q:G40 4.49 Mg OP2 Q:G40 2.20 Mg O5' Q:G40 4.45 Mg C3' Q:U71 3.91 Mg O3' Q:U71 2.76 Mg C5' Q:U71 4.44 Mg C2' Q:U71 4.61 Mg C4' Q:U71 3.97 Mg O2' Q:U71 4.06 Mg O Q:Hoh93 3.17 interactive model: Magnesium binding site 2 out of 7 in 2oiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2oiu. 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: Q: G1, Q: U71, Q: Hoh88, Q: Hoh91, conact list: Atom Atom Distance (A) Mg C6 Q:G1 3.30 Mg N1 Q:G1 4.37 Mg C5 Q:G1 4.06 Mg N7 Q:G1 4.09 Mg O6 Q:G1 2.18 Mg C5 Q:U71 4.81 Mg O4 Q:U71 4.67 Mg O Q:Hoh88 3.14 Mg O Q:Hoh91 3.18 interactive model: Magnesium binding site 3 out of 7 in 2oiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2oiu. 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: Q: G1, Q: U50, Q: U71, Q: Hoh91, conact list: Atom Atom Distance (A) Mg N2 Q:G1 3.25 Mg C2 Q:G1 3.78 Mg C6 Q:G1 4.35 Mg N1 Q:G1 3.27 Mg O6 Q:G1 4.47 Mg N3 Q:U50 4.34 Mg C6 Q:U50 4.52 Mg C5 Q:U50 3.66 Mg C4 Q:U50 3.52 Mg O4 Q:U50 3.35 Mg O4 Q:U71 4.87 Mg O Q:Hoh91 3.09 interactive model: Magnesium binding site 4 out of 7 in 2oiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2oiu. 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: Q: G11, Q: A13, Q: Hoh87, conact list: Atom Atom Distance (A) Mg C8 Q:G11 4.79 Mg C6 Q:G11 3.61 Mg N1 Q:G11 4.71 Mg C5 Q:G11 3.90 Mg N7 Q:G11 3.67 Mg O6 Q:G11 2.93 Mg OP1 Q:A13 4.29 Mg OP2 Q:A13 4.88 Mg O Q:Hoh87 4.76 interactive model: Magnesium binding site 5 out of 7 in 2oiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 2oiu. 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: conact list: Atom Atom Distance (A) interactive model: Magnesium binding site 6 out of 7 in 2oiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 2oiu. 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: Q: G52, Q: G53, Q: Hoh79, conact list: Atom Atom Distance (A) Mg N3 Q:G52 4.25 Mg N2 Q:G52 4.63 Mg C2 Q:G52 4.89 Mg C1' Q:G52 4.73 Mg C2' Q:G52 3.90 Mg O2' Q:G52 3.20 Mg C3' Q:G53 4.97 Mg C1' Q:G53 4.01 Mg O4' Q:G53 2.98 Mg C5' Q:G53 3.84 Mg C2' Q:G53 4.96 Mg C4' Q:G53 3.56 Mg O5' Q:G53 4.57 Mg O Q:Hoh79 2.89 interactive model: Magnesium binding site 7 out of 7 in 2oiu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 2oiu. 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: Q: G1, Q: G52, Q: G53, Q: U54, Q: C70, Q: U71, Q: Hoh83, Q: Hoh94, conact list: Atom Atom Distance (A) Mg N2 Q:G1 4.95 Mg C8 Q:G52 4.79 Mg C6 Q:G52 3.85 Mg C5 Q:G52 4.06 Mg N7 Q:G52 3.67 Mg O6 Q:G52 3.16 Mg C8 Q:G53 4.90 Mg C6 Q:G53 3.54 Mg N1 Q:G53 4.80 Mg C5 Q:G53 3.93 Mg N7 Q:G53 3.63 Mg O6 Q:G53 2.65 Mg O4 Q:U54 4.42 Mg N4 Q:C70 4.05 Mg N3 Q:U71 4.77 Mg O4 Q:U71 4.45 Mg O Q:Hoh83 2.85 Mg O Q:Hoh94 4.68 interactive model: