Magnesium in the structure of Rna Polymerase II Elongation Complex At 5 Mm MG2+ With Gtp (pdb 2e2h)

The binding sites of Magnesium atom in the structure of Rna Polymerase II Elongation Complex At 5 Mm MG2+ With Gtp (pdb code 2e2h). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2e2h structure was solved by D.WANG, D.A.BUSHNELL, K.D.WESTOVER, C.D.KAPLAN, R.D.KORNBERG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 45.1-4.0 Space group C121 a (A) 171.108 b (A) 222.005 c (A) 195.163 alpha (°) 90.00 beta (°) 102.61 gamma (°) 90.00 Rfactor (%) 29 Rfree (%) 36.8 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 2e2h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2e2h. 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: R: A10, A: Asp481, A: Asp483, A: Asp485, A: Mg2002, T: Gtp3000, conact list: Atom Atom Distance (A) Mg C3' R:A10 4.08 Mg C5' R:A10 4.49 Mg C4' R:A10 4.45 Mg O5' R:A10 4.84 Mg N A:Asp481 4.66 Mg CB A:Asp481 3.31 Mg OD2 A:Asp481 4.48 Mg OD1 A:Asp481 2.94 Mg CG A:Asp481 3.41 Mg CA A:Asp481 4.54 Mg N A:Asp483 4.83 Mg CB A:Asp483 4.10 Mg OD2 A:Asp483 2.32 Mg OD1 A:Asp483 2.21 Mg CG A:Asp483 2.57 Mg CA A:Asp483 4.90 Mg CB A:Asp485 4.67 Mg OD2 A:Asp485 3.94 Mg OD1 A:Asp485 2.24 Mg CG A:Asp485 3.42 Mg MG A:Mg2002 3.43 Mg PG T:Gtp3000 4.79 Mg O2G T:Gtp3000 4.56 Mg PA T:Gtp3000 2.72 Mg C4' T:Gtp3000 4.68 Mg O5' T:Gtp3000 4.12 Mg O3A T:Gtp3000 3.58 Mg O3G T:Gtp3000 3.94 Mg O2A T:Gtp3000 2.02 Mg PB T:Gtp3000 4.99 Mg C5' T:Gtp3000 4.50 Mg O1A T:Gtp3000 2.49 interactive model: Magnesium binding site 2 out of 2 in 2e2h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2e2h. 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: Asp481, A: Asp483, B: Asp837, B: Arg1020, A: Mg2001, T: Gtp3000, conact list: Atom Atom Distance (A) Mg CB A:Asp481 3.54 Mg OD2 A:Asp481 4.15 Mg OD1 A:Asp481 2.19 Mg CG A:Asp481 3.11 Mg CB A:Asp483 4.11 Mg OD2 A:Asp483 4.25 Mg OD1 A:Asp483 2.22 Mg CG A:Asp483 3.35 Mg CB B:Asp837 3.81 Mg OD2 B:Asp837 4.39 Mg OD1 B:Asp837 2.25 Mg CG B:Asp837 3.34 Mg CZ B:Arg1020 4.06 Mg NH2 B:Arg1020 4.20 Mg NH1 B:Arg1020 3.12 Mg MG A:Mg2001 3.43 Mg PG T:Gtp3000 3.44 Mg O3B T:Gtp3000 4.06 Mg O2G T:Gtp3000 4.25 Mg PA T:Gtp3000 3.71 Mg O2B T:Gtp3000 3.13 Mg O3A T:Gtp3000 3.06 Mg O3G T:Gtp3000 1.97 Mg O2A T:Gtp3000 4.07 Mg PB T:Gtp3000 3.60 Mg O1G T:Gtp3000 4.33 Mg O1A T:Gtp3000 3.55 interactive model: