Magnesium in the structure of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna With A 2'5'-Phosphodiester Linkage (pdb 3b4c)

The binding sites of Magnesium atom in the structure of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna With A 2'5'-Phosphodiester Linkage (pdb code 3b4c). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3b4c structure was solved by D.J.KLEIN, A.R.FERRE-D'AMARE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-3.0 Space group P21212 a (A) 178.300 b (A) 40.400 c (A) 77.500 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.8 Rfree (%) 26.2 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 3b4c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3b4c. 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: G1, A: C2, B: A35, B: C36, B: G37, B: Hoh402, A: Hoh401, conact list: Atom Atom Distance (A) Mg C3' A:G1 4.85 Mg O3' A:G1 3.51 Mg O2' A:G1 4.59 Mg OP1 A:C2 4.95 Mg P A:C2 3.68 Mg OP2 A:C2 2.64 Mg C5' A:C2 4.08 Mg O5' A:C2 4.40 Mg C3' B:A35 3.94 Mg O3' B:A35 2.68 Mg C2' B:A35 4.48 Mg O2' B:A35 3.83 Mg OP1 B:C36 4.10 Mg C3' B:C36 4.44 Mg P B:C36 2.88 Mg O3' B:C36 4.63 Mg OP2 B:C36 1.97 Mg C5' B:C36 4.64 Mg O5' B:C36 3.81 Mg OP1 B:G37 4.18 Mg P B:G37 3.80 Mg OP2 B:G37 2.58 Mg O B:Hoh402 2.06 Mg O A:Hoh401 1.83 interactive model: Magnesium binding site 2 out of 4 in 3b4c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3b4c. 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: C2, A: G3, B: C63, B: G64, B: G65, A: Glp201, conact list: Atom Atom Distance (A) Mg N4 A:C2 4.89 Mg O6 A:G3 4.55 Mg C5 B:C63 4.22 Mg C4 B:C63 4.20 Mg N4 B:C63 3.52 Mg C8 B:G64 4.89 Mg C6 B:G64 3.54 Mg N1 B:G64 4.82 Mg C5 B:G64 3.94 Mg N7 B:G64 3.63 Mg O6 B:G64 2.61 Mg O6 B:G65 4.42 Mg C6 A:Glp201 4.00 Mg P A:Glp201 3.58 Mg O3P A:Glp201 3.07 Mg O1P A:Glp201 4.84 Mg O2P A:Glp201 2.94 Mg O6 A:Glp201 4.36 interactive model: Magnesium binding site 3 out of 4 in 3b4c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3b4c. 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: C2, B: G37, B: A38, B: G39, conact list: Atom Atom Distance (A) Mg OP1 A:C2 3.33 Mg P A:C2 4.71 Mg C3' B:G37 4.28 Mg O3' B:G37 4.51 Mg OP1 B:A38 4.93 Mg C8 B:A38 4.05 Mg P B:A38 3.76 Mg N7 B:A38 3.90 Mg OP2 B:A38 2.42 Mg O5' B:A38 4.07 Mg C6 B:G39 4.31 Mg C5 B:G39 4.48 Mg N7 B:G39 3.92 Mg O6 B:G39 3.50 interactive model: Magnesium binding site 4 out of 4 in 3b4c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3b4c. 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: G1, B: A35, B: C52, B: G53, conact list: Atom Atom Distance (A) Mg C8 A:G1 4.99 Mg C5 A:G1 4.96 Mg N7 A:G1 4.04 Mg O6 A:G1 4.54 Mg C2 B:A35 4.96 Mg N1 B:A35 4.72 Mg N4 B:C52 4.65 Mg O6 B:G53 4.90 interactive model: