Manganese in the structure of Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution (pdb 3dky)

The binding sites of Manganese atom in the structure of Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution (pdb code 3dky). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3dky structure was solved by D.R.BOER, J.A.RUIZ-MASO, A.G.BLANCO, M.VIVES-LLACER, I.USON, F.X.GOMIS-RUTH, M.ESPINOSA, G.DEL SOLAR, M.COLL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.6-3.6 Space group P43 a (A) 91.460 b (A) 91.460 c (A) 227.080 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.3 Rfree (%) 25.7 Manganese Binding Sites: Manganese binding site 1 out of 4 in 3dky Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3dky. 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: His39, A: Asp42, A: His55, A: His57, A: Tyr99, A: His102, conact list: Atom Atom Distance (A) Mn NE2 A:His39 4.19 Mn CB A:His39 4.16 Mn ND1 A:His39 2.77 Mn CD2 A:His39 4.41 Mn CE1 A:His39 3.24 Mn CG A:His39 3.64 Mn CB A:Asp42 4.64 Mn OD2 A:Asp42 3.61 Mn OD1 A:Asp42 2.57 Mn CG A:Asp42 3.36 Mn NE2 A:His55 2.54 Mn ND1 A:His55 4.26 Mn CD2 A:His55 3.82 Mn CE1 A:His55 2.98 Mn CG A:His55 4.69 Mn NE2 A:His57 2.78 Mn ND1 A:His57 4.89 Mn CD2 A:His57 3.40 Mn CE1 A:His57 3.93 Mn CG A:His57 4.67 Mn CE1 A:Tyr99 4.69 Mn OH A:Tyr99 4.52 Mn NE2 A:His102 3.91 Mn CE1 A:His102 3.98 interactive model: Manganese binding site 2 out of 4 in 3dky Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3dky. 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: His39, B: Asp42, B: His55, B: His57, B: His102, conact list: Atom Atom Distance (A) Mn NE2 B:His39 3.96 Mn CB B:His39 3.68 Mn ND1 B:His39 2.49 Mn CD2 B:His39 4.04 Mn CE1 B:His39 3.09 Mn CG B:His39 3.22 Mn CB B:Asp42 4.79 Mn OD2 B:Asp42 3.57 Mn OD1 B:Asp42 2.84 Mn CG B:Asp42 3.49 Mn NE2 B:His55 2.15 Mn ND1 B:His55 3.87 Mn CD2 B:His55 3.41 Mn CE1 B:His55 2.62 Mn CG B:His55 4.27 Mn NE2 B:His57 2.65 Mn ND1 B:His57 4.72 Mn CD2 B:His57 3.11 Mn CE1 B:His57 3.85 Mn CG B:His57 4.39 Mn NE2 B:His102 4.29 Mn CE1 B:His102 4.20 interactive model: Manganese binding site 3 out of 4 in 3dky Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3dky. 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: His39, C: Asp42, C: His55, C: His57, C: Tyr99, C: His102, conact list: Atom Atom Distance (A) Mn NE2 C:His39 4.03 Mn CB C:His39 3.76 Mn ND1 C:His39 2.43 Mn CD2 C:His39 4.15 Mn CE1 C:His39 3.06 Mn CG C:His39 3.28 Mn CB C:Asp42 4.59 Mn OD2 C:Asp42 3.33 Mn OD1 C:Asp42 2.55 Mn CG C:Asp42 3.24 Mn NE2 C:His55 2.41 Mn ND1 C:His55 4.09 Mn CD2 C:His55 3.69 Mn CE1 C:His55 2.81 Mn CG C:His55 4.54 Mn NE2 C:His57 2.91 Mn ND1 C:His57 4.99 Mn CD2 C:His57 3.33 Mn CE1 C:His57 4.12 Mn CG C:His57 4.63 Mn CE1 C:Tyr99 4.90 Mn OH C:Tyr99 4.89 Mn NE2 C:His102 4.02 Mn CE1 C:His102 3.93 interactive model: Manganese binding site 4 out of 4 in 3dky Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3dky. 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: F: His39, F: Asp42, F: His55, F: His57, F: Tyr99, F: His102, conact list: Atom Atom Distance (A) Mn NE2 F:His39 4.21 Mn CB F:His39 4.07 Mn ND1 F:His39 2.70 Mn CD2 F:His39 4.39 Mn CE1 F:His39 3.23 Mn CG F:His39 3.57 Mn CB F:Asp42 4.75 Mn OD2 F:Asp42 3.63 Mn OD1 F:Asp42 2.68 Mn CG F:Asp42 3.45 Mn NE2 F:His55 2.49 Mn ND1 F:His55 4.22 Mn CD2 F:His55 3.77 Mn CE1 F:His55 2.94 Mn CG F:His55 4.64 Mn NE2 F:His57 2.71 Mn ND1 F:His57 4.83 Mn CD2 F:His57 3.27 Mn CE1 F:His57 3.89 Mn CG F:His57 4.56 Mn CE1 F:Tyr99 4.72 Mn OH F:Tyr99 4.66 Mn NE2 F:His102 3.99 Mn CE1 F:His102 4.04 interactive model: