Manganese in the structure of Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima (pdb 2glf)

The binding sites of Manganese atom in the structure of Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima (pdb code 2glf). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2glf structure was solved by T.MIN, L.SHAPIRO, S.K.BURLEY, NEW YORK SGX RESEARCH CENTER FORSTRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.8-2.8 Space group P213 a (A) 191.225 b (A) 191.225 c (A) 191.225 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.8 Rfree (%) 23.9 Manganese Binding Sites: Manganese binding site 1 out of 8 in 2glf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2glf. 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: His94, A: Asp251, A: Asp252, A: Glu280, A: Glu281, A: Asp328, A: Val329, A: Mse426, A: Mn5002, A: Hoh5079, conact list: Atom Atom Distance (A) Mn NE2 A:His94 2.44 Mn ND1 A:His94 4.54 Mn CD2 A:His94 3.41 Mn CE1 A:His94 3.40 Mn CG A:His94 4.57 Mn O A:Asp251 4.81 Mn CB A:Asp251 4.69 Mn OD2 A:Asp251 3.56 Mn C A:Asp251 4.72 Mn OD1 A:Asp251 2.32 Mn CG A:Asp251 3.30 Mn N A:Asp252 4.91 Mn CB A:Asp252 4.28 Mn OD2 A:Asp252 4.95 Mn OD1 A:Asp252 4.51 Mn CG A:Asp252 4.42 Mn OE1 A:Glu280 3.59 Mn CD A:Glu280 4.43 Mn CG A:Glu280 4.75 Mn OE2 A:Glu281 3.93 Mn CD A:Glu281 4.82 Mn CB A:Asp328 4.34 Mn OD2 A:Asp328 2.40 Mn OD1 A:Asp328 2.55 Mn CG A:Asp328 2.82 Mn N A:Val329 4.91 Mn CG2 A:Val329 4.63 Mn CE A:Mse426 4.62 Mn MN A:Mn5002 3.34 Mn O A:Hoh5079 2.36 interactive model: Manganese binding site 2 out of 8 in 2glf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2glf. 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: His94, A: Pro98, A: Asp251, A: Glu280, A: Glu281, A: Mse426, A: His427, D: His169, A: Mn5001, A: Hoh5072, A: Hoh5079, conact list: Atom Atom Distance (A) Mn NE2 A:His94 4.45 Mn CE1 A:His94 4.50 Mn CD A:Pro98 4.89 Mn CB A:Asp251 4.40 Mn OD2 A:Asp251 2.41 Mn OD1 A:Asp251 3.40 Mn CG A:Asp251 3.15 Mn OE1 A:Glu280 3.98 Mn OE1 A:Glu281 2.64 Mn OE2 A:Glu281 2.04 Mn CD A:Glu281 2.67 Mn CG A:Glu281 4.15 Mn SE A:Mse426 4.99 Mn CE A:Mse426 3.35 Mn NE2 A:His427 2.42 Mn ND1 A:His427 4.52 Mn CD2 A:His427 3.37 Mn CE1 A:His427 3.40 Mn CG A:His427 4.54 Mn NE2 D:His169 4.65 Mn CE1 D:His169 4.62 Mn MN A:Mn5001 3.34 Mn O A:Hoh5072 4.87 Mn O A:Hoh5079 3.89 interactive model: Manganese binding site 3 out of 8 in 2glf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2glf. 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: His94, B: Pro98, B: Asp251, B: Glu280, B: Glu281, B: Mse426, B: His427, B: Mn5004, B: Hoh5072, conact list: Atom Atom Distance (A) Mn NE2 B:His94 4.46 Mn CE1 B:His94 4.40 Mn CD B:Pro98 4.65 Mn CG B:Pro98 4.75 Mn CB B:Asp251 4.36 Mn OD2 B:Asp251 2.26 Mn OD1 B:Asp251 3.48 Mn CG B:Asp251 3.13 Mn OE1 B:Glu280 4.18 Mn OE1 B:Glu281 2.56 Mn OE2 B:Glu281 2.18 Mn CD B:Glu281 2.69 Mn CG B:Glu281 4.19 Mn CE B:Mse426 3.43 Mn NE2 B:His427 2.22 Mn ND1 B:His427 4.30 Mn CD2 B:His427 3.22 Mn CE1 B:His427 3.18 Mn CG B:His427 4.36 Mn MN B:Mn5004 3.48 Mn O B:Hoh5072 2.22 interactive model: Manganese binding site 4 out of 8 in 2glf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2glf. 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: His94, B: Asp251, B: Asp252, B: Glu280, B: Glu281, B: Asp328, B: Val329, B: Mse426, B: Mn5003, B: Hoh5064, B: Hoh5072, conact list: Atom Atom Distance (A) Mn NE2 B:His94 2.32 Mn ND1 B:His94 4.40 Mn CD2 B:His94 3.31 Mn CE1 B:His94 3.27 Mn CG B:His94 4.45 Mn O B:Asp251 4.78 Mn CB B:Asp251 4.63 Mn OD2 B:Asp251 3.50 Mn C B:Asp251 4.74 Mn OD1 B:Asp251 2.27 Mn CG B:Asp251 3.25 Mn CB B:Asp252 4.52 Mn OD2 B:Asp252 4.82 Mn OD1 B:Asp252 4.74 Mn CG B:Asp252 4.52 Mn OE1 B:Glu280 3.62 Mn CD B:Glu280 4.53 Mn CG B:Glu280 4.93 Mn OE2 B:Glu281 4.45 Mn CB B:Asp328 4.17 Mn OD2 B:Asp328 2.04 Mn OD1 B:Asp328 2.70 Mn CG B:Asp328 2.70 Mn CA B:Asp328 4.72 Mn N B:Val329 4.82 Mn CG2 B:Val329 4.91 Mn CE B:Mse426 4.23 Mn MN B:Mn5003 3.48 Mn O B:Hoh5064 4.26 Mn O B:Hoh5072 2.85 interactive model: Manganese binding site 5 out of 8 in 2glf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 2glf. 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: His94, C: Asp251, C: Asp252, C: Glu280, C: Glu281, C: Asp328, C: Val329, C: Mse426, C: Mn5007, C: Hoh5019, C: Hoh5058, conact list: Atom Atom Distance (A) Mn NE2 C:His94 2.29 Mn ND1 C:His94 4.25 Mn CD2 C:His94 3.45 Mn CE1 C:His94 3.03 Mn CG C:His94 4.48 Mn O C:Asp251 4.90 Mn CB C:Asp251 4.65 Mn OD2 C:Asp251 3.57 Mn C C:Asp251 4.78 Mn OD1 C:Asp251 2.28 Mn CG C:Asp251 3.28 Mn N C:Asp252 4.97 Mn CB C:Asp252 4.52 Mn OD1 C:Asp252 4.23 Mn CG C:Asp252 4.43 Mn OE1 C:Glu280 3.21 Mn OE2 C:Glu280 4.96 Mn CD C:Glu280 4.16 Mn CG C:Glu280 4.81 Mn OE1 C:Glu281 4.04 Mn CD C:Glu281 4.75 Mn CB C:Asp328 4.31 Mn OD2 C:Asp328 2.27 Mn OD1 C:Asp328 2.65 Mn CG C:Asp328 2.80 Mn CA C:Asp328 4.98 Mn N C:Val329 4.82 Mn CG2 C:Val329 4.76 Mn CE C:Mse426 4.77 Mn MN C:Mn5007 3.33 Mn O C:Hoh5019 4.62 Mn O C:Hoh5058 3.91 interactive model: Manganese binding site 6 out of 8 in 2glf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 2glf. 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: His94, C: Pro98, C: Asp251, C: Glu280, C: Glu281, C: Mse426, C: His427, C: Mn5006, C: Hoh5009, C: Hoh5058, conact list: Atom Atom Distance (A) Mn NE2 C:His94 4.64 Mn CE1 C:His94 4.48 Mn CD C:Pro98 5.00 Mn CG C:Pro98 4.98 Mn CB C:Asp251 4.55 Mn OD2 C:Asp251 2.57 Mn OD1 C:Asp251 3.47 Mn CG C:Asp251 3.28 Mn OE1 C:Glu280 3.67 Mn CD C:Glu280 4.90 Mn OE1 C:Glu281 2.13 Mn OE2 C:Glu281 2.59 Mn CD C:Glu281 2.67 Mn CG C:Glu281 4.16 Mn CE C:Mse426 3.55 Mn NE2 C:His427 2.40 Mn ND1 C:His427 4.45 Mn CD2 C:His427 3.36 Mn CE1 C:His427 3.34 Mn CG C:His427 4.50 Mn MN C:Mn5006 3.33 Mn O C:Hoh5009 4.53 Mn O C:Hoh5058 3.73 interactive model: Manganese binding site 7 out of 8 in 2glf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 2glf. 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: His94, D: Asp251, D: Asp252, D: Glu280, D: Glu281, D: Asp328, D: Val329, D: Mse426, D: Mn5009, D: Hoh5026, D: Hoh5083, D: Hoh5096, conact list: Atom Atom Distance (A) Mn NE2 D:His94 2.31 Mn ND1 D:His94 4.40 Mn CD2 D:His94 3.28 Mn CE1 D:His94 3.28 Mn CG D:His94 4.43 Mn O D:Asp251 4.86 Mn CB D:Asp251 4.59 Mn OD2 D:Asp251 3.77 Mn C D:Asp251 4.67 Mn OD1 D:Asp251 2.20 Mn CG D:Asp251 3.32 Mn CA D:Asp251 4.95 Mn N D:Asp252 4.82 Mn CB D:Asp252 4.38 Mn OD2 D:Asp252 4.75 Mn OD1 D:Asp252 4.17 Mn CG D:Asp252 4.25 Mn OE1 D:Glu280 3.49 Mn CD D:Glu280 4.40 Mn CG D:Glu280 4.89 Mn OE1 D:Glu281 4.14 Mn CB D:Asp328 4.26 Mn OD2 D:Asp328 2.19 Mn OD1 D:Asp328 2.68 Mn CG D:Asp328 2.76 Mn CA D:Asp328 4.90 Mn N D:Val329 4.57 Mn CG2 D:Val329 4.19 Mn CE D:Mse426 4.71 Mn MN D:Mn5009 3.59 Mn O D:Hoh5026 4.66 Mn O D:Hoh5083 2.06 Mn O D:Hoh5096 3.52 interactive model: Manganese binding site 8 out of 8 in 2glf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 2glf. 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: His169, D: His94, D: Pro98, D: Asp251, D: Glu280, D: Glu281, D: Mse426, D: His427, D: Mn5008, D: Hoh5026, D: Hoh5032, D: Hoh5083, D: Hoh5096, conact list: Atom Atom Distance (A) Mn NE2 A:His169 4.74 Mn CE1 A:His169 4.55 Mn NE2 D:His94 4.59 Mn CE1 D:His94 4.57 Mn CD D:Pro98 4.76 Mn CG D:Pro98 4.96 Mn CB D:Asp251 4.33 Mn OD2 D:Asp251 2.52 Mn OD1 D:Asp251 3.26 Mn CG D:Asp251 3.10 Mn OE1 D:Glu280 3.99 Mn OE1 D:Glu281 2.12 Mn OE2 D:Glu281 2.79 Mn CD D:Glu281 2.80 Mn CG D:Glu281 4.28 Mn CE D:Mse426 3.37 Mn NE2 D:His427 2.33 Mn ND1 D:His427 4.45 Mn CD2 D:His427 3.19 Mn CE1 D:His427 3.38 Mn CG D:His427 4.40 Mn MN D:Mn5008 3.59 Mn O D:Hoh5026 4.72 Mn O D:Hoh5032 4.60 Mn O D:Hoh5083 3.31 Mn O D:Hoh5096 2.25 interactive model: