Manganese in the structure of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine (pdb 3mx6)

The binding sites of Manganese atom in the structure of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine (pdb code 3mx6). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3mx6 structure was solved by SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.7 Space group P1211 a (A) 50.370 b (A) 67.550 c (A) 80.890 alpha (°) 90.00 beta (°) 97.43 gamma (°) 90.00 Rfactor (%) 16.8 Rfree (%) 20.7 Manganese Binding Sites: Manganese binding site 1 out of 4 in 3mx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3mx6. 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: Asp105, A: His168, A: Phe174, A: His175, A: Thr199, A: Glu201, A: Glu233, A: Met262, A: Mn260, A: Hoh532, A: Hoh623, conact list: Atom Atom Distance (A) Mn CB A:Asp105 4.39 Mn OD2 A:Asp105 2.25 Mn OD1 A:Asp105 3.59 Mn CG A:Asp105 3.20 Mn NE2 A:His168 2.14 Mn ND1 A:His168 4.25 Mn CD2 A:His168 3.07 Mn CE1 A:His168 3.16 Mn CG A:His168 4.24 Mn CE1 A:Phe174 4.86 Mn NE2 A:His175 4.63 Mn CD2 A:His175 4.90 Mn CB A:Thr199 4.24 Mn CG2 A:Thr199 4.05 Mn OG1 A:Thr199 3.82 Mn OE1 A:Glu201 2.18 Mn CB A:Glu201 4.99 Mn OE2 A:Glu201 3.44 Mn CD A:Glu201 3.09 Mn CG A:Glu201 4.36 Mn OE1 A:Glu233 3.42 Mn OE2 A:Glu233 2.18 Mn CD A:Glu233 3.14 Mn CG A:Glu233 4.52 Mn O A:Met262 2.21 Mn N A:Met262 4.82 Mn CB A:Met262 4.92 Mn C A:Met262 2.66 Mn CA A:Met262 4.13 Mn OXT A:Met262 2.45 Mn MN A:Mn260 3.47 Mn O A:Hoh532 4.51 Mn O A:Hoh623 4.23 interactive model: Manganese binding site 2 out of 4 in 3mx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3mx6. 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: Asp94, A: Val95, A: Thr96, A: Asp105, A: Thr106, A: Glu201, A: Glu233, A: Met262, A: Mn259, A: Hoh263, A: Hoh463, A: Hoh532, A: Hoh535, conact list: Atom Atom Distance (A) Mn CB A:Asp94 4.19 Mn OD2 A:Asp94 2.55 Mn C A:Asp94 4.95 Mn OD1 A:Asp94 2.08 Mn CG A:Asp94 2.65 Mn CA A:Asp94 4.91 Mn O A:Val95 4.37 Mn N A:Val95 4.92 Mn OG1 A:Thr96 3.92 Mn CB A:Asp105 4.44 Mn OD2 A:Asp105 3.30 Mn C A:Asp105 4.77 Mn OD1 A:Asp105 2.07 Mn CG A:Asp105 3.05 Mn CA A:Asp105 4.85 Mn O A:Thr106 4.80 Mn N A:Thr106 4.51 Mn C A:Thr106 4.89 Mn OE1 A:Glu201 4.97 Mn OE2 A:Glu201 4.87 Mn OE1 A:Glu233 2.27 Mn CB A:Glu233 4.88 Mn OE2 A:Glu233 3.46 Mn CD A:Glu233 3.17 Mn CG A:Glu233 4.47 Mn O A:Met262 2.14 Mn N A:Met262 3.65 Mn CB A:Met262 4.57 Mn C A:Met262 3.20 Mn CA A:Met262 3.97 Mn OXT A:Met262 4.06 Mn MN A:Mn259 3.47 Mn O A:Hoh263 3.79 Mn O A:Hoh463 4.31 Mn O A:Hoh532 2.28 Mn O A:Hoh535 4.32 interactive model: Manganese binding site 3 out of 4 in 3mx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3mx6. 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: Asp105, B: His168, B: Phe174, B: His175, B: Thr199, B: Glu201, B: Glu233, B: Met262, B: Mn260, B: Hoh496, B: Hoh625, conact list: Atom Atom Distance (A) Mn CB B:Asp105 4.36 Mn OD2 B:Asp105 2.26 Mn OD1 B:Asp105 3.56 Mn CG B:Asp105 3.18 Mn NE2 B:His168 2.13 Mn ND1 B:His168 4.23 Mn CD2 B:His168 3.08 Mn CE1 B:His168 3.14 Mn CG B:His168 4.25 Mn CE1 B:Phe174 4.85 Mn NE2 B:His175 4.58 Mn CD2 B:His175 4.88 Mn CB B:Thr199 4.24 Mn CG2 B:Thr199 4.02 Mn OG1 B:Thr199 3.79 Mn OE1 B:Glu201 2.19 Mn OE2 B:Glu201 3.45 Mn CD B:Glu201 3.12 Mn CG B:Glu201 4.40 Mn OE1 B:Glu233 3.49 Mn OE2 B:Glu233 2.15 Mn CD B:Glu233 3.16 Mn CG B:Glu233 4.49 Mn O B:Met262 2.18 Mn N B:Met262 4.83 Mn CB B:Met262 4.96 Mn C B:Met262 2.64 Mn CA B:Met262 4.13 Mn OXT B:Met262 2.36 Mn MN B:Mn260 3.50 Mn O B:Hoh496 4.53 Mn O B:Hoh625 4.18 interactive model: Manganese binding site 4 out of 4 in 3mx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3mx6. 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: Asp94, B: Val95, B: Thr96, B: Asp105, B: Thr106, B: Glu201, B: Glu233, B: Met262, B: Mn259, B: Hoh282, B: Hoh346, B: Hoh392, B: Hoh496, conact list: Atom Atom Distance (A) Mn CB B:Asp94 4.11 Mn OD2 B:Asp94 2.41 Mn C B:Asp94 4.91 Mn OD1 B:Asp94 2.05 Mn CG B:Asp94 2.56 Mn CA B:Asp94 4.85 Mn O B:Val95 4.40 Mn N B:Val95 4.93 Mn C B:Val95 4.98 Mn OG1 B:Thr96 3.88 Mn CB B:Asp105 4.43 Mn OD2 B:Asp105 3.36 Mn C B:Asp105 4.73 Mn OD1 B:Asp105 2.07 Mn CG B:Asp105 3.07 Mn CA B:Asp105 4.81 Mn O B:Thr106 4.76 Mn N B:Thr106 4.48 Mn C B:Thr106 4.88 Mn OE1 B:Glu201 4.99 Mn OE2 B:Glu201 4.94 Mn OE1 B:Glu233 2.23 Mn CB B:Glu233 4.87 Mn OE2 B:Glu233 3.41 Mn CD B:Glu233 3.13 Mn CG B:Glu233 4.46 Mn O B:Met262 2.16 Mn N B:Met262 3.71 Mn CB B:Met262 4.60 Mn C B:Met262 3.22 Mn CA B:Met262 3.98 Mn OXT B:Met262 4.08 Mn MN B:Mn259 3.50 Mn O B:Hoh282 3.90 Mn O B:Hoh346 4.31 Mn O B:Hoh392 4.29 Mn O B:Hoh496 2.27 interactive model: