Manganese in the structure of Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition At the Cleavage Site (pdb 1eo4)

The binding sites of Manganese atom in the structure of Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition At the Cleavage Site (pdb code 1eo4). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1eo4 structure was solved by N.C.HORTON, B.A.CONNOLLY, J.J.PERONA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 4.9-1.9 Space group P1 a (A) 47.700 b (A) 48.500 c (A) 63.700 alpha (°) 96.70 beta (°) 109.60 gamma (°) 106.30 Rfactor (%) 21.3 Rfree (%) 30.5 Manganese Binding Sites: Manganese binding site 1 out of 5 in 1eo4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1eo4. 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: Glu45, A: Glu65, A: Pro66, A: Asp74, B: Asp36, A: Hoh617, A: Hoh618, A: Hoh619, A: Hoh678, A: Hoh680, A: Hoh686, B: Hoh698, B: Hoh699, B: Hoh709, conact list: Atom Atom Distance (A) Mn OE1 A:Glu45 3.98 Mn OE2 A:Glu45 2.33 Mn CD A:Glu45 3.48 Mn CG A:Glu45 4.69 Mn OE2 A:Glu65 4.50 Mn CD A:Pro66 4.93 Mn O A:Asp74 4.25 Mn CB A:Asp74 3.76 Mn OD2 A:Asp74 4.18 Mn C A:Asp74 4.56 Mn OD1 A:Asp74 2.84 Mn CG A:Asp74 3.39 Mn CA A:Asp74 3.87 Mn OD1 B:Asp36 4.98 Mn O A:Hoh617 4.40 Mn O A:Hoh618 4.59 Mn O A:Hoh619 1.98 Mn O A:Hoh678 2.05 Mn O A:Hoh680 4.22 Mn O A:Hoh686 2.04 Mn O B:Hoh698 2.05 Mn O B:Hoh699 3.94 Mn O B:Hoh709 3.39 interactive model: Manganese binding site 2 out of 5 in 1eo4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1eo4. 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: Lys102, A: Ile103, A: His193, A: Hoh622, A: Hoh624, A: Hoh663, A: Hoh687, A: Hoh709, A: Hoh710, A: Hoh719, A: Hoh730, A: Hoh731, A: Hoh732, conact list: Atom Atom Distance (A) Mn O A:Lys102 3.27 Mn CB A:Lys102 4.22 Mn C A:Lys102 3.97 Mn CA A:Lys102 4.61 Mn N A:Ile103 4.70 Mn CA A:Ile103 4.87 Mn NE2 A:His193 2.32 Mn ND1 A:His193 4.45 Mn CD2 A:His193 3.33 Mn CE1 A:His193 3.29 Mn CG A:His193 4.49 Mn O A:Hoh622 3.79 Mn O A:Hoh624 2.10 Mn O A:Hoh663 4.60 Mn O A:Hoh687 2.00 Mn O A:Hoh709 4.19 Mn O A:Hoh710 1.98 Mn O A:Hoh719 2.07 Mn O A:Hoh730 4.62 Mn O A:Hoh731 4.45 Mn O A:Hoh732 3.63 interactive model: Manganese binding site 3 out of 5 in 1eo4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1eo4. 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: D: Dt10, A: His71, A: Thr118, A: Asn120, A: Hoh607, A: Hoh689, A: Hoh706, conact list: Atom Atom Distance (A) Mn O3' D:Dt10 4.93 Mn NE2 A:His71 2.18 Mn ND1 A:His71 4.33 Mn CD2 A:His71 3.20 Mn CE1 A:His71 3.19 Mn CG A:His71 4.36 Mn O A:Thr118 4.52 Mn N A:Asn120 4.44 Mn CA A:Asn120 4.76 Mn O A:Hoh607 2.00 Mn O A:Hoh689 2.15 Mn O A:Hoh706 2.03 interactive model: Manganese binding site 4 out of 5 in 1eo4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1eo4. 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: C: Da7, C: Dt8, A: Glu45, A: Asp74, A: Asp90, A: Ile91, A: Lys92, C: Hoh23, C: Hoh172, A: Hoh618, A: Hoh619, A: Hoh646, A: Hoh659, A: Hoh662, conact list: Atom Atom Distance (A) Mn C3' C:Da7 4.68 Mn O3' C:Da7 4.67 Mn OP2 C:Da7 4.68 Mn C5' C:Da7 4.39 Mn C4' C:Da7 4.57 Mn OP1 C:Dt8 4.66 Mn OE1 A:Glu45 2.81 Mn OE2 A:Glu45 4.44 Mn CD A:Glu45 3.89 Mn CG A:Glu45 4.95 Mn CB A:Asp74 4.49 Mn OD2 A:Asp74 2.19 Mn OD1 A:Asp74 3.30 Mn CG A:Asp74 3.11 Mn OD2 A:Asp90 4.58 Mn C A:Asp90 4.98 Mn OD1 A:Asp90 4.52 Mn CG A:Asp90 4.69 Mn O A:Ile91 2.44 Mn N A:Ile91 3.93 Mn CB A:Ile91 3.97 Mn CG2 A:Ile91 4.93 Mn C A:Ile91 3.51 Mn CA A:Ile91 3.99 Mn N A:Lys92 4.67 Mn O C:Hoh23 2.11 Mn O C:Hoh172 4.55 Mn O A:Hoh618 2.05 Mn O A:Hoh619 3.80 Mn O A:Hoh646 3.80 Mn O A:Hoh659 4.39 Mn O A:Hoh662 1.99 interactive model: Manganese binding site 5 out of 5 in 1eo4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 1eo4. 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: C: Dt10, C: Dt11, B: His71, B: Thr118, B: Asn120, B: Ile121, C: Hoh84, C: Hoh184, B: Hoh622, conact list: Atom Atom Distance (A) Mn O3' C:Dt10 4.38 Mn OP1 C:Dt11 2.22 Mn P C:Dt11 3.69 Mn OP2 C:Dt11 4.66 Mn C5' C:Dt11 4.14 Mn O5' C:Dt11 4.34 Mn NE2 B:His71 2.31 Mn ND1 B:His71 4.44 Mn CD2 B:His71 3.18 Mn CE1 B:His71 3.37 Mn CG B:His71 4.38 Mn O B:Thr118 4.32 Mn N B:Asn120 4.40 Mn CA B:Asn120 4.79 Mn O B:Ile121 4.84 Mn O C:Hoh84 2.00 Mn O C:Hoh184 1.95 Mn O B:Hoh622 2.15 interactive model: