Manganese in the structure of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed With MN2+, Pep, and Phe (pdb 1kfl)

The binding sites of Manganese atom in the structure of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed With MN2+, Pep, and Phe (pdb code 1kfl). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1kfl structure was solved by I.A.SHUMILIN, C.ZHAO, R.BAUERLE, R.H.KRETSINGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.8 Space group C121 a (A) 290.097 b (A) 90.097 c (A) 155.798 alpha (°) 90.00 beta (°) 120.77 gamma (°) 90.00 Rfactor (%) 21.8 Rfree (%) 24.6 Manganese Binding Sites: Manganese binding site 1 out of 8 in 1kfl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1kfl. 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: Cys61, A: Arg92, A: Lys97, A: His268, A: Glu302, A: Asp326, A: Pep1352, conact list: Atom Atom Distance (A) Mn O A:Cys61 4.61 Mn CB A:Cys61 3.77 Mn SG A:Cys61 2.65 Mn C A:Cys61 4.81 Mn CA A:Cys61 4.30 Mn CZ A:Arg92 4.65 Mn NH2 A:Arg92 3.70 Mn CE A:Lys97 4.52 Mn CD A:Lys97 4.08 Mn NZ A:Lys97 3.95 Mn NE2 A:His268 2.38 Mn ND1 A:His268 4.44 Mn CD2 A:His268 3.29 Mn CE1 A:His268 3.36 Mn CG A:His268 4.45 Mn OE1 A:Glu302 3.16 Mn OE2 A:Glu302 2.10 Mn CD A:Glu302 2.95 Mn CG A:Glu302 4.34 Mn N A:Asp326 4.90 Mn CB A:Asp326 3.47 Mn OD2 A:Asp326 2.07 Mn OD1 A:Asp326 4.11 Mn CG A:Asp326 3.03 Mn CA A:Asp326 4.79 Mn O2 A:Pep1352 4.68 Mn P A:Pep1352 4.89 Mn O1P A:Pep1352 4.95 Mn O2P A:Pep1352 4.15 interactive model: Manganese binding site 2 out of 8 in 1kfl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1kfl. 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: Cys61, B: Arg92, B: Lys97, B: His268, B: Glu302, B: Asp326, B: Pep2352, conact list: Atom Atom Distance (A) Mn O B:Cys61 4.44 Mn CB B:Cys61 3.78 Mn SG B:Cys61 2.80 Mn C B:Cys61 4.66 Mn CA B:Cys61 4.22 Mn CZ B:Arg92 4.32 Mn NE B:Arg92 4.97 Mn NH2 B:Arg92 3.35 Mn CE B:Lys97 4.59 Mn CD B:Lys97 4.18 Mn NZ B:Lys97 4.13 Mn NE2 B:His268 2.51 Mn ND1 B:His268 4.47 Mn CD2 B:His268 3.50 Mn CE1 B:His268 3.34 Mn CG B:His268 4.58 Mn OE1 B:Glu302 3.24 Mn OE2 B:Glu302 2.14 Mn CD B:Glu302 3.01 Mn CG B:Glu302 4.38 Mn CB B:Asp326 3.72 Mn OD2 B:Asp326 2.34 Mn OD1 B:Asp326 4.38 Mn CG B:Asp326 3.31 Mn O2 B:Pep2352 4.53 Mn P B:Pep2352 4.77 Mn O1P B:Pep2352 4.96 Mn O2P B:Pep2352 3.96 interactive model: Manganese binding site 3 out of 8 in 1kfl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1kfl. 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: Cys61, C: Arg92, C: Lys97, C: His268, C: Glu302, C: Asp326, C: Pep3352, conact list: Atom Atom Distance (A) Mn O C:Cys61 4.76 Mn CB C:Cys61 3.94 Mn SG C:Cys61 2.79 Mn C C:Cys61 4.94 Mn CA C:Cys61 4.45 Mn CZ C:Arg92 4.74 Mn NH2 C:Arg92 3.77 Mn CE C:Lys97 4.43 Mn CD C:Lys97 4.14 Mn NZ C:Lys97 3.93 Mn NE2 C:His268 2.45 Mn ND1 C:His268 4.41 Mn CD2 C:His268 3.34 Mn CE1 C:His268 3.35 Mn CG C:His268 4.43 Mn OE1 C:Glu302 3.23 Mn OE2 C:Glu302 2.27 Mn CD C:Glu302 3.08 Mn CG C:Glu302 4.48 Mn N C:Asp326 4.95 Mn CB C:Asp326 3.52 Mn OD2 C:Asp326 2.07 Mn OD1 C:Asp326 4.11 Mn CG C:Asp326 3.05 Mn CA C:Asp326 4.84 Mn O2 C:Pep3352 4.57 Mn P C:Pep3352 4.90 Mn O2P C:Pep3352 4.20 interactive model: Manganese binding site 4 out of 8 in 1kfl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1kfl. 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: Cys61, D: Arg92, D: Lys97, D: His268, D: Glu302, D: Asp326, D: Pep4352, conact list: Atom Atom Distance (A) Mn O D:Cys61 4.65 Mn CB D:Cys61 3.82 Mn SG D:Cys61 2.63 Mn C D:Cys61 4.87 Mn CA D:Cys61 4.39 Mn CZ D:Arg92 4.65 Mn NH2 D:Arg92 3.71 Mn CE D:Lys97 4.53 Mn CD D:Lys97 4.19 Mn NZ D:Lys97 4.01 Mn NE2 D:His268 2.29 Mn ND1 D:His268 4.35 Mn CD2 D:His268 3.19 Mn CE1 D:His268 3.27 Mn CG D:His268 4.34 Mn OE1 D:Glu302 3.08 Mn OE2 D:Glu302 2.19 Mn CD D:Glu302 2.96 Mn CG D:Glu302 4.36 Mn N D:Asp326 4.99 Mn CB D:Asp326 3.51 Mn OD2 D:Asp326 2.10 Mn OD1 D:Asp326 4.09 Mn CG D:Asp326 3.04 Mn CA D:Asp326 4.85 Mn O2 D:Pep4352 4.53 Mn P D:Pep4352 4.84 Mn O1P D:Pep4352 4.98 Mn O2P D:Pep4352 4.13 interactive model: Manganese binding site 5 out of 8 in 1kfl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 1kfl. 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: E: Cys61, E: Arg92, E: Lys97, E: His268, E: Glu302, E: Asp326, E: Pep5352, conact list: Atom Atom Distance (A) Mn O E:Cys61 4.68 Mn CB E:Cys61 3.80 Mn SG E:Cys61 2.80 Mn C E:Cys61 4.89 Mn CA E:Cys61 4.37 Mn CZ E:Arg92 4.65 Mn NH2 E:Arg92 3.76 Mn CE E:Lys97 4.57 Mn CD E:Lys97 4.25 Mn NZ E:Lys97 4.04 Mn NE2 E:His268 2.37 Mn ND1 E:His268 4.40 Mn CD2 E:His268 3.23 Mn CE1 E:His268 3.35 Mn CG E:His268 4.37 Mn OE1 E:Glu302 3.15 Mn OE2 E:Glu302 2.21 Mn CD E:Glu302 3.00 Mn CG E:Glu302 4.41 Mn CB E:Asp326 3.50 Mn OD2 E:Asp326 2.09 Mn OD1 E:Asp326 4.16 Mn CG E:Asp326 3.08 Mn CA E:Asp326 4.85 Mn O2 E:Pep5352 4.56 Mn P E:Pep5352 4.93 Mn O2P E:Pep5352 4.22 interactive model: Manganese binding site 6 out of 8 in 1kfl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 1kfl. 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: Cys61, F: Arg92, F: Lys97, F: His268, F: Glu302, F: Asp326, F: Pep6352, conact list: Atom Atom Distance (A) Mn O F:Cys61 4.54 Mn CB F:Cys61 3.76 Mn SG F:Cys61 2.72 Mn C F:Cys61 4.75 Mn CA F:Cys61 4.30 Mn CZ F:Arg92 4.63 Mn NH2 F:Arg92 3.65 Mn CE F:Lys97 4.44 Mn CD F:Lys97 4.12 Mn NZ F:Lys97 3.92 Mn NE2 F:His268 2.55 Mn ND1 F:His268 4.53 Mn CD2 F:His268 3.43 Mn CE1 F:His268 3.47 Mn CG F:His268 4.54 Mn OE1 F:Glu302 3.25 Mn OE2 F:Glu302 2.22 Mn CD F:Glu302 3.07 Mn CG F:Glu302 4.46 Mn N F:Asp326 4.93 Mn CB F:Asp326 3.54 Mn OD2 F:Asp326 2.04 Mn OD1 F:Asp326 4.04 Mn CG F:Asp326 3.02 Mn CA F:Asp326 4.84 Mn O2 F:Pep6352 4.60 Mn P F:Pep6352 4.91 Mn O2P F:Pep6352 4.15 interactive model: Manganese binding site 7 out of 8 in 1kfl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 1kfl. 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: G: Cys61, G: Arg92, G: Lys97, G: His268, G: Glu302, G: Asp326, G: Pep7352, conact list: Atom Atom Distance (A) Mn O G:Cys61 4.76 Mn CB G:Cys61 3.81 Mn SG G:Cys61 2.91 Mn C G:Cys61 4.94 Mn CA G:Cys61 4.40 Mn CZ G:Arg92 4.67 Mn NH2 G:Arg92 3.76 Mn CE G:Lys97 4.48 Mn CD G:Lys97 4.23 Mn NZ G:Lys97 3.87 Mn NE2 G:His268 2.38 Mn ND1 G:His268 4.31 Mn CD2 G:His268 3.30 Mn CE1 G:His268 3.24 Mn CG G:His268 4.37 Mn OE1 G:Glu302 3.20 Mn OE2 G:Glu302 2.15 Mn CD G:Glu302 3.00 Mn CG G:Glu302 4.39 Mn CB G:Asp326 3.53 Mn OD2 G:Asp326 2.06 Mn OD1 G:Asp326 4.12 Mn CG G:Asp326 3.06 Mn CA G:Asp326 4.89 Mn O2 G:Pep7352 4.54 Mn P G:Pep7352 4.93 Mn O2P G:Pep7352 4.30 interactive model: Manganese binding site 8 out of 8 in 1kfl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 1kfl. 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: H: Cys61, H: Arg92, H: Lys97, H: His268, H: Glu302, H: Asp326, H: Pep8352, conact list: Atom Atom Distance (A) Mn O H:Cys61 4.60 Mn CB H:Cys61 3.77 Mn SG H:Cys61 2.69 Mn C H:Cys61 4.79 Mn CA H:Cys61 4.27 Mn CZ H:Arg92 4.58 Mn NH2 H:Arg92 3.65 Mn CE H:Lys97 4.53 Mn CD H:Lys97 4.20 Mn NZ H:Lys97 4.07 Mn NE2 H:His268 2.36 Mn ND1 H:His268 4.35 Mn CD2 H:His268 3.30 Mn CE1 H:His268 3.27 Mn CG H:His268 4.40 Mn OE1 H:Glu302 3.19 Mn OE2 H:Glu302 2.10 Mn CD H:Glu302 2.97 Mn CG H:Glu302 4.35 Mn N H:Asp326 4.97 Mn CB H:Asp326 3.52 Mn OD2 H:Asp326 2.20 Mn OD1 H:Asp326 4.26 Mn CG H:Asp326 3.16 Mn CA H:Asp326 4.84 Mn O2 H:Pep8352 4.60 Mn P H:Pep8352 4.90 Mn O1P H:Pep8352 4.98 Mn O2P H:Pep8352 4.20 interactive model: