Magnesium in the structure of Structural Basis For The Interaction of Antibiotics With the Peptidyl Transferase Center in Eubacteria (pdb 1jzz)

The binding sites of Magnesium atom in the structure of Structural Basis For The Interaction of Antibiotics With the Peptidyl Transferase Center in Eubacteria (pdb code 1jzz). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1jzz structure was solved by F.SCHLUENZEN, R.ZARIVACH, J.HARMS, A.BASHAN, A.TOCILJ, R.ALBRECHT, A.YONATH, F.FRANCESCHI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-3.8 Space group I222 a (A) 170.400 b (A) 410.700 c (A) 694.800 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.9 Rfree (%) 27.4 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 1jzz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1jzz. 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: A2045, A: C2420, A: C2421, A: Rox2881, conact list: Atom Atom Distance (A) Mg N9 A:A2045 4.97 Mg N3 A:A2045 4.01 Mg C2 A:A2045 4.64 Mg C1' A:A2045 4.58 Mg C4 A:A2045 4.72 Mg C2' A:A2045 4.84 Mg O2' A:A2045 4.32 Mg OP1 A:C2420 3.91 Mg P A:C2420 4.84 Mg O3' A:C2420 4.87 Mg OP2 A:C2420 4.85 Mg C5' A:C2420 4.91 Mg OP1 A:C2421 4.50 Mg C38 A:Rox2881 4.45 Mg O14 A:Rox2881 4.79 Mg C39 A:Rox2881 4.21 interactive model: Magnesium binding site 2 out of 2 in 1jzz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1jzz. 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: A2430, A: C2431, A: U2485, A: U2564, conact list: Atom Atom Distance (A) Mg N3 A:A2430 4.59 Mg C2 A:A2430 4.84 Mg C2' A:A2430 4.95 Mg O2' A:A2430 4.79 Mg O4' A:C2431 4.81 Mg N1 A:U2485 4.87 Mg C1' A:U2485 4.53 Mg O4' A:U2485 4.41 Mg N3 A:U2564 4.48 Mg O4 A:U2564 4.62 interactive model: