Manganese in the structure of Structural Explanation For The Role Of Mn in the Activity of PHI6 Rna-Dependent Rna Polymerase (pdb 2jlf)

The binding sites of Manganese atom in the structure of Structural Explanation For The Role Of Mn in the Activity of PHI6 Rna-Dependent Rna Polymerase (pdb code 2jlf). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2jlf structure was solved by M.M.PORANEN, P.S.SALGADO, M.R.L.KOIVUNEN, S.WRIGHT, D.H.BAMFORD, D.I.STUART, J.M.GRIMES, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 18.0-3.2 Space group P32 a (A) 110.040 b (A) 110.040 c (A) 159.132 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 22.75 Rfree (%) 28.6 Manganese Binding Sites: Manganese binding site 1 out of 2 in 2jlf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2jlf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ala322, A: Thr323, A: Asp454, A: Ala455, A: Gln491, A: Ala495, A: Phe496, conact list: Atom Atom Distance (A) Mn C A:Ala322 5.00 Mn CB A:Ala322 4.42 Mn CA A:Ala322 4.98 Mn O A:Thr323 3.57 Mn N A:Thr323 4.86 Mn C A:Thr323 4.75 Mn CB A:Asp454 4.55 Mn OD2 A:Asp454 3.79 Mn OD1 A:Asp454 2.15 Mn CG A:Asp454 3.30 Mn CA A:Asp454 4.68 Mn O A:Ala455 3.99 Mn N A:Ala455 4.39 Mn C A:Ala455 4.84 Mn NE2 A:Gln491 2.86 Mn OE1 A:Gln491 2.36 Mn CB A:Gln491 4.28 Mn CD A:Gln491 2.78 Mn CG A:Gln491 4.04 Mn O A:Ala495 2.47 Mn N A:Ala495 4.25 Mn C A:Ala495 3.66 Mn CA A:Ala495 4.58 Mn N A:Phe496 4.54 Mn CA A:Phe496 4.52 interactive model: Manganese binding site 2 out of 2 in 2jlf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2jlf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Ala322, B: Thr323, B: Asp454, B: Ala455, B: Gln491, B: Ala495, B: Phe496, conact list: Atom Atom Distance (A) Mn C B:Ala322 4.82 Mn CB B:Ala322 4.30 Mn CA B:Ala322 4.89 Mn O B:Thr323 3.33 Mn N B:Thr323 4.74 Mn C B:Thr323 4.52 Mn CB B:Asp454 4.76 Mn OD2 B:Asp454 4.06 Mn OD1 B:Asp454 2.40 Mn CG B:Asp454 3.55 Mn CA B:Asp454 4.84 Mn O B:Ala455 4.17 Mn N B:Ala455 4.59 Mn NE2 B:Gln491 2.58 Mn OE1 B:Gln491 2.22 Mn CB B:Gln491 3.96 Mn CD B:Gln491 2.50 Mn CG B:Gln491 3.73 Mn O B:Ala495 2.69 Mn N B:Ala495 4.28 Mn C B:Ala495 3.87 Mn CA B:Ala495 4.70 Mn N B:Phe496 4.82 Mn CA B:Phe496 4.86 interactive model: