Manganese in the structure of Crystal Structure of Poliovirus Polymerase Complexed With Ctp and MN2+ (pdb 2im1)

The binding sites of Manganese atom in the structure of Crystal Structure of Poliovirus Polymerase Complexed With Ctp and MN2+ (pdb code 2im1). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2im1 structure was solved by A.A.THOMPSON, O.B.PEERSEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.2-2.5 Space group P65 a (A) 128.942 b (A) 128.942 c (A) 112.979 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.9 Rfree (%) 26.8 Manganese Binding Sites: Manganese binding site 1 out of 3 in 2im1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2im1. 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: Asp233, A: Asp328, A: Asp329, A: Mn2002, A: Hoh549, conact list: Atom Atom Distance (A) Mn CB A:Asp233 4.86 Mn OD2 A:Asp328 3.13 Mn OD1 A:Asp328 4.29 Mn CG A:Asp328 4.00 Mn N A:Asp329 4.74 Mn CB A:Asp329 4.66 Mn OD2 A:Asp329 4.09 Mn CG A:Asp329 4.57 Mn CA A:Asp329 4.75 Mn MN A:Mn2002 3.71 Mn O A:Hoh549 3.74 interactive model: Manganese binding site 2 out of 3 in 2im1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2im1. 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: Asp233, A: Tyr234, A: Asp328, A: Mn2001, A: Mn2003, A: Ctp1001, A: Hoh549, conact list: Atom Atom Distance (A) Mn CB A:Asp233 4.51 Mn O A:Tyr234 3.24 Mn C A:Tyr234 4.47 Mn OD2 A:Asp328 4.20 Mn MN A:Mn2001 3.71 Mn MN A:Mn2003 4.28 Mn PG A:Ctp1001 3.64 Mn O3B A:Ctp1001 3.37 Mn O2G A:Ctp1001 4.46 Mn PA A:Ctp1001 4.85 Mn O3G A:Ctp1001 2.92 Mn O1B A:Ctp1001 4.28 Mn PB A:Ctp1001 3.30 Mn O2B A:Ctp1001 2.30 Mn O3A A:Ctp1001 4.57 Mn O1A A:Ctp1001 3.84 Mn O A:Hoh549 3.16 interactive model: Manganese binding site 3 out of 3 in 2im1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2im1. 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: Lys167, A: Lys359, A: Mn2002, A: Ctp1001, A: Hoh549, A: Hoh617, conact list: Atom Atom Distance (A) Mn CE A:Lys167 3.58 Mn CD A:Lys167 4.64 Mn NZ A:Lys167 2.13 Mn CE A:Lys359 4.16 Mn NZ A:Lys359 3.84 Mn MN A:Mn2002 4.28 Mn PG A:Ctp1001 3.28 Mn O3B A:Ctp1001 2.49 Mn O2G A:Ctp1001 2.80 Mn PA A:Ctp1001 3.40 Mn O3G A:Ctp1001 4.21 Mn O2A A:Ctp1001 3.98 Mn PB A:Ctp1001 3.75 Mn O5' A:Ctp1001 4.79 Mn O2B A:Ctp1001 4.26 Mn O3A A:Ctp1001 3.97 Mn O1G A:Ctp1001 4.47 Mn O1A A:Ctp1001 2.73 Mn O A:Hoh549 3.42 Mn O A:Hoh617 3.49 interactive model: