Manganese in the structure of S.Pombe MRE11 Apoenzym (pdb 4fcx)

The binding sites of Manganese atom in the structure of S.Pombe MRE11 Apoenzym (pdb code 4fcx). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 4fcx structure was solved by C.B.SCHILLER, K.LAMMENS, K.P.HOPFNER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 21.8-3.0 Space group P212121 a (A) 76.408 b (A) 82.262 c (A) 164.296 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.7 Rfree (%) 28.6 Manganese Binding Sites: Manganese binding site 1 out of 4 in 4fcx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 4fcx. 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: Asp25, B: His27, B: Asp65, B: Asn133, B: His222, B: His250, B: His252, B: Mn502, conact list: Atom Atom Distance (A) Mn CB B:Asp25 4.04 Mn OD2 B:Asp25 2.24 Mn OD1 B:Asp25 4.40 Mn CG B:Asp25 3.41 Mn CA B:Asp25 4.97 Mn NE2 B:His27 2.50 Mn ND1 B:His27 4.57 Mn CD2 B:His27 3.47 Mn CE1 B:His27 3.43 Mn CG B:His27 4.61 Mn CB B:Asp65 3.77 Mn OD2 B:Asp65 4.45 Mn OD1 B:Asp65 2.46 Mn CG B:Asp65 3.40 Mn OD1 B:Asn133 4.74 Mn NE2 B:His222 4.50 Mn CE1 B:His222 4.60 Mn O B:His250 3.64 Mn C B:His250 4.54 Mn CA B:His250 4.65 Mn NE2 B:His252 2.39 Mn ND1 B:His252 4.47 Mn CD2 B:His252 3.21 Mn CE1 B:His252 3.42 Mn CG B:His252 4.39 Mn MN B:Mn502 3.16 interactive model: Manganese binding site 2 out of 4 in 4fcx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 4fcx. 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: Asp25, B: Asp65, B: Asn133, B: His222, B: His250, B: Mn501, conact list: Atom Atom Distance (A) Mn OD2 B:Asp25 4.00 Mn CB B:Asp65 4.46 Mn OD2 B:Asp65 3.92 Mn OD1 B:Asp65 2.26 Mn CG B:Asp65 3.35 Mn N B:Asn133 4.46 Mn CB B:Asn133 4.48 Mn ND2 B:Asn133 2.49 Mn OD1 B:Asn133 2.85 Mn CG B:Asn133 3.02 Mn NE2 B:His222 2.47 Mn ND1 B:His222 4.44 Mn CD2 B:His222 3.31 Mn CE1 B:His222 3.41 Mn CG B:His222 4.43 Mn O B:His250 4.03 Mn NE2 B:His250 4.41 Mn N B:His250 4.63 Mn CB B:His250 3.97 Mn ND1 B:His250 2.50 Mn CD2 B:His250 4.58 Mn C B:His250 4.33 Mn CE1 B:His250 3.25 Mn CG B:His250 3.56 Mn CA B:His250 3.67 Mn MN B:Mn501 3.16 interactive model: Manganese binding site 3 out of 4 in 4fcx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 4fcx. 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: Asp25, A: Asp65, A: Asn133, A: His222, A: His250, A: Mn502, conact list: Atom Atom Distance (A) Mn OD2 A:Asp25 4.00 Mn CB A:Asp65 4.49 Mn OD2 A:Asp65 2.25 Mn OD1 A:Asp65 3.58 Mn CG A:Asp65 3.22 Mn N A:Asn133 4.75 Mn ND2 A:Asn133 2.85 Mn OD1 A:Asn133 4.34 Mn CG A:Asn133 3.96 Mn NE2 A:His222 3.12 Mn ND1 A:His222 3.60 Mn CD2 A:His222 4.40 Mn CE1 A:His222 2.48 Mn CG A:His222 4.64 Mn O A:His250 4.51 Mn NE2 A:His250 4.45 Mn CB A:His250 3.98 Mn ND1 A:His250 2.49 Mn CD2 A:His250 4.63 Mn C A:His250 4.77 Mn CE1 A:His250 3.26 Mn CG A:His250 3.59 Mn CA A:His250 4.02 Mn MN A:Mn502 3.13 interactive model: Manganese binding site 4 out of 4 in 4fcx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 4fcx. 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: Asp25, A: His27, A: Asp65, A: His222, A: His250, A: His252, A: Mn501, conact list: Atom Atom Distance (A) Mn CB A:Asp25 4.05 Mn OD2 A:Asp25 2.35 Mn OD1 A:Asp25 4.52 Mn CG A:Asp25 3.49 Mn NE2 A:His27 2.53 Mn ND1 A:His27 4.61 Mn CD2 A:His27 3.48 Mn CE1 A:His27 3.48 Mn CG A:His27 4.65 Mn CB A:Asp65 3.69 Mn OD2 A:Asp65 2.26 Mn OD1 A:Asp65 4.36 Mn CG A:Asp65 3.29 Mn NE2 A:His222 4.58 Mn CE1 A:His222 4.82 Mn O A:His250 4.94 Mn ND1 A:His250 4.86 Mn CA A:His250 4.80 Mn NE2 A:His252 2.42 Mn ND1 A:His252 4.56 Mn CD2 A:His252 3.20 Mn CE1 A:His252 3.51 Mn CG A:His252 4.43 Mn MN A:Mn501 3.13 interactive model: