Manganese in the structure of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex With Reduced Nrdi (pdb 3n3a)

The binding sites of Manganese atom in the structure of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex With Reduced Nrdi (pdb code 3n3a). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3n3a structure was solved by A.K.BOAL, J.A.COTRUVO JR., J.STUBBE, A.C.ROSENZWEIG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.6-2.0 Space group P212121 a (A) 74.863 b (A) 90.678 c (A) 143.837 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.3 Rfree (%) 22.7 Manganese Binding Sites: Manganese binding site 1 out of 4 in 3n3a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3n3a. 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: Gln70, B: Ile94, B: Glu98, B: His101, B: Glu158, B: Glu192, B: His195, B: Mn321, B: Hoh338, B: Hoh348, B: Hoh429, B: Hoh440, conact list: Atom Atom Distance (A) Mn OE1 B:Gln70 4.39 Mn CG2 B:Ile94 4.59 Mn OE1 B:Glu98 3.24 Mn OE2 B:Glu98 2.08 Mn CD B:Glu98 3.01 Mn CG B:Glu98 4.40 Mn CE1 B:His101 4.83 Mn OE1 B:Glu158 3.59 Mn CB B:Glu158 4.36 Mn OE2 B:Glu158 2.16 Mn CD B:Glu158 3.11 Mn CG B:Glu158 4.25 Mn OE1 B:Glu192 2.24 Mn CB B:Glu192 4.95 Mn OE2 B:Glu192 2.32 Mn CD B:Glu192 2.61 Mn CG B:Glu192 4.14 Mn CA B:Glu192 4.86 Mn NE2 B:His195 4.39 Mn CB B:His195 3.54 Mn ND1 B:His195 2.31 Mn CD2 B:His195 4.43 Mn CE1 B:His195 3.27 Mn CG B:His195 3.29 Mn MN B:Mn321 3.70 Mn O B:Hoh338 4.65 Mn O B:Hoh348 3.88 Mn O B:Hoh429 2.22 Mn O B:Hoh440 4.20 interactive model: Manganese binding site 2 out of 4 in 3n3a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3n3a. 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: Asp67, B: Glu98, B: His101, B: Glu158, B: Phe162, B: Ile188, B: Glu192, B: His195, B: Mn320, B: Hoh430, conact list: Atom Atom Distance (A) Mn CB B:Asp67 4.51 Mn OD2 B:Asp67 3.51 Mn OD1 B:Asp67 2.14 Mn CG B:Asp67 3.17 Mn OE1 B:Glu98 2.14 Mn CB B:Glu98 4.66 Mn OE2 B:Glu98 3.81 Mn CD B:Glu98 3.30 Mn CG B:Glu98 4.55 Mn CA B:Glu98 4.41 Mn NE2 B:His101 4.23 Mn CB B:His101 3.80 Mn ND1 B:His101 2.23 Mn CD2 B:His101 4.41 Mn CE1 B:His101 3.03 Mn CG B:His101 3.36 Mn OE1 B:Glu158 2.23 Mn OE2 B:Glu158 3.50 Mn CD B:Glu158 3.20 Mn CG B:Glu158 4.55 Mn CZ B:Phe162 4.99 Mn CE1 B:Phe162 4.89 Mn CG2 B:Ile188 4.75 Mn OE1 B:Glu192 4.14 Mn OE2 B:Glu192 2.23 Mn CD B:Glu192 3.22 Mn CG B:Glu192 3.85 Mn ND1 B:His195 4.94 Mn MN B:Mn320 3.70 Mn O B:Hoh430 2.27 interactive model: Manganese binding site 3 out of 4 in 3n3a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3n3a. 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: Gln70, A: Ile94, A: Glu98, A: His101, A: Glu158, A: Glu192, A: His195, A: Mn321, A: Hoh347, A: Hoh388, A: Hoh391, A: Hoh412, conact list: Atom Atom Distance (A) Mn OE1 A:Gln70 4.38 Mn CG2 A:Ile94 4.56 Mn OE1 A:Glu98 3.19 Mn OE2 A:Glu98 2.11 Mn CD A:Glu98 2.99 Mn CG A:Glu98 4.41 Mn CE1 A:His101 4.89 Mn OE1 A:Glu158 3.52 Mn CB A:Glu158 4.40 Mn OE2 A:Glu158 2.23 Mn CD A:Glu158 3.11 Mn CG A:Glu158 4.28 Mn OE1 A:Glu192 2.19 Mn CB A:Glu192 4.91 Mn OE2 A:Glu192 2.40 Mn CD A:Glu192 2.63 Mn CG A:Glu192 4.16 Mn CA A:Glu192 4.83 Mn NE2 A:His195 4.33 Mn CB A:His195 3.61 Mn ND1 A:His195 2.27 Mn CD2 A:His195 4.41 Mn CE1 A:His195 3.17 Mn CG A:His195 3.30 Mn MN A:Mn321 3.70 Mn O A:Hoh347 4.04 Mn O A:Hoh388 2.26 Mn O A:Hoh391 4.24 Mn O A:Hoh412 4.79 interactive model: Manganese binding site 4 out of 4 in 3n3a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3n3a. 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: Asp67, A: Glu98, A: His101, A: Glu158, A: Phe162, A: Ile188, A: Glu192, A: His195, A: Mn320, A: Hoh401, conact list: Atom Atom Distance (A) Mn CB A:Asp67 4.48 Mn OD2 A:Asp67 3.55 Mn OD1 A:Asp67 2.08 Mn CG A:Asp67 3.16 Mn CA A:Asp67 4.94 Mn OE1 A:Glu98 2.20 Mn CB A:Glu98 4.67 Mn OE2 A:Glu98 3.91 Mn CD A:Glu98 3.37 Mn CG A:Glu98 4.59 Mn CA A:Glu98 4.40 Mn NE2 A:His101 4.32 Mn CB A:His101 3.80 Mn ND1 A:His101 2.30 Mn CD2 A:His101 4.47 Mn CE1 A:His101 3.13 Mn CG A:His101 3.41 Mn OE1 A:Glu158 2.23 Mn OE2 A:Glu158 3.56 Mn CD A:Glu158 3.24 Mn CG A:Glu158 4.57 Mn CZ A:Phe162 4.97 Mn CE1 A:Phe162 4.90 Mn CG2 A:Ile188 4.71 Mn OE1 A:Glu192 4.05 Mn OE2 A:Glu192 2.15 Mn CD A:Glu192 3.15 Mn CG A:Glu192 3.83 Mn ND1 A:His195 5.00 Mn MN A:Mn320 3.70 Mn O A:Hoh401 2.27 interactive model: