Manganese in the structure of Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense (pdb 3god)

The binding sites of Manganese atom in the structure of Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense (pdb code 3god). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3god structure was solved by B.WIEDENHEFT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 18.0-2.2 Space group P212121 a (A) 109.870 b (A) 110.960 c (A) 130.250 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.3 Rfree (%) 25.8 Manganese Binding Sites: Manganese binding site 1 out of 4 in 3god Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3god. 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: Arg140, A: Glu190, A: His254, A: Asp268, A: Lys271, A: Hoh362, A: Hoh437, A: Hoh451, A: Hoh487, A: Hoh526, A: Hoh662, conact list: Atom Atom Distance (A) Mn CZ A:Arg140 4.79 Mn NH2 A:Arg140 4.42 Mn NH1 A:Arg140 4.17 Mn OE1 A:Glu190 2.50 Mn OE2 A:Glu190 3.15 Mn CD A:Glu190 3.01 Mn CG A:Glu190 4.27 Mn NE2 A:His254 2.28 Mn ND1 A:His254 3.95 Mn CD2 A:His254 3.46 Mn CE1 A:His254 2.76 Mn CG A:His254 4.31 Mn CB A:Asp268 4.53 Mn OD2 A:Asp268 2.38 Mn OD1 A:Asp268 2.92 Mn CG A:Asp268 3.04 Mn NZ A:Lys271 4.75 Mn O A:Hoh362 3.84 Mn O A:Hoh437 4.32 Mn O A:Hoh451 2.47 Mn O A:Hoh487 4.68 Mn O A:Hoh526 2.45 Mn O A:Hoh662 3.93 interactive model: Manganese binding site 2 out of 4 in 3god Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3god. 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: Arg140, B: Glu190, B: His254, B: Asp268, B: Hoh348, B: Hoh436, B: Hoh535, conact list: Atom Atom Distance (A) Mn CZ B:Arg140 4.63 Mn NH2 B:Arg140 4.39 Mn NH1 B:Arg140 3.93 Mn OE1 B:Glu190 2.28 Mn OE2 B:Glu190 3.09 Mn CD B:Glu190 2.88 Mn CG B:Glu190 4.15 Mn NE2 B:His254 2.40 Mn ND1 B:His254 4.13 Mn CD2 B:His254 3.58 Mn CE1 B:His254 2.92 Mn CG B:His254 4.47 Mn CB B:Asp268 4.52 Mn OD2 B:Asp268 2.40 Mn OD1 B:Asp268 2.99 Mn CG B:Asp268 3.07 Mn O B:Hoh348 4.04 Mn O B:Hoh436 4.15 Mn O B:Hoh535 4.78 interactive model: Manganese binding site 3 out of 4 in 3god Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3god. 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: Glu190, C: His254, C: Asp268, C: Hoh506, C: Hoh508, C: Hoh553, conact list: Atom Atom Distance (A) Mn OE1 C:Glu190 4.96 Mn NE2 C:His254 2.72 Mn ND1 C:His254 4.48 Mn CD2 C:His254 3.83 Mn CE1 C:His254 3.30 Mn CG C:His254 4.77 Mn OD2 C:Asp268 3.62 Mn OD1 C:Asp268 4.38 Mn CG C:Asp268 4.44 Mn O C:Hoh506 2.43 Mn O C:Hoh508 3.80 Mn O C:Hoh553 4.16 interactive model: Manganese binding site 4 out of 4 in 3god Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3god. 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: Glu190, D: His254, D: Asp268, D: Lys271, conact list: Atom Atom Distance (A) Mn OE1 D:Glu190 4.81 Mn OE2 D:Glu190 4.82 Mn NE2 D:His254 2.78 Mn ND1 D:His254 4.46 Mn CD2 D:His254 3.84 Mn CE1 D:His254 3.33 Mn CG D:His254 4.75 Mn OD2 D:Asp268 3.55 Mn OD1 D:Asp268 4.40 Mn CG D:Asp268 4.38 Mn NZ D:Lys271 4.73 interactive model: