Manganese in the structure of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida (pdb 3h8g)

The binding sites of Manganese atom in the structure of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida (pdb code 3h8g). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3h8g structure was solved by A.KALE, B.W.DIJKSTRA, T.SONKE, A.M.W.H.THUNNISSEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 38.6-1.5 Space group P1 a (A) 95.976 b (A) 95.989 c (A) 95.998 alpha (°) 100.82 beta (°) 107.78 gamma (°) 93.23 Rfactor (%) 14.9 Rfree (%) 17.3 Manganese Binding Sites: Manganese binding site 1 out of 6 in 3h8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3h8g. 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: Asp272, A: Gly274, A: Lys279, A: Asp290, A: Asn322, A: Asp349, A: Ala350, A: Glu351, A: Zn501, A: Bct504, A: Bes505, conact list: Atom Atom Distance (A) Mn CB A:Asp272 4.43 Mn OD2 A:Asp272 2.17 Mn OD1 A:Asp272 3.24 Mn CG A:Asp272 3.05 Mn CA A:Gly274 4.84 Mn CE A:Lys279 4.10 Mn NZ A:Lys279 3.84 Mn OD2 A:Asp290 4.90 Mn ND2 A:Asn322 4.71 Mn O A:Asp349 2.18 Mn N A:Asp349 4.93 Mn CB A:Asp349 3.83 Mn OD2 A:Asp349 3.91 Mn C A:Asp349 3.11 Mn OD1 A:Asp349 2.08 Mn CG A:Asp349 3.04 Mn CA A:Asp349 3.54 Mn N A:Ala350 4.28 Mn CA A:Ala350 4.71 Mn N A:Glu351 4.34 Mn OE1 A:Glu351 2.14 Mn CB A:Glu351 4.94 Mn OE2 A:Glu351 3.39 Mn CD A:Glu351 3.12 Mn CG A:Glu351 4.49 Mn ZN A:Zn501 3.28 Mn O1 A:Bct504 3.97 Mn O2 A:Bct504 4.76 Mn C A:Bct504 4.72 Mn N2 A:Bes505 4.23 Mn C1 A:Bes505 3.83 Mn O3 A:Bes505 2.44 Mn C2 A:Bes505 3.09 Mn N1 A:Bes505 4.14 Mn O2 A:Bes505 2.15 Mn C4 A:Bes505 4.81 Mn C3 A:Bes505 3.00 interactive model: Manganese binding site 2 out of 6 in 3h8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3h8g. 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: Asp272, B: Gly274, B: Lys279, B: Asp290, B: Asn322, B: Asp349, B: Ala350, B: Glu351, B: Zn501, B: Bct504, B: Bes505, conact list: Atom Atom Distance (A) Mn CB B:Asp272 4.44 Mn OD2 B:Asp272 2.14 Mn OD1 B:Asp272 3.24 Mn CG B:Asp272 3.03 Mn CA B:Gly274 4.90 Mn CE B:Lys279 4.07 Mn NZ B:Lys279 3.85 Mn OD2 B:Asp290 4.91 Mn ND2 B:Asn322 4.73 Mn O B:Asp349 2.20 Mn N B:Asp349 4.96 Mn CB B:Asp349 3.82 Mn OD2 B:Asp349 3.92 Mn C B:Asp349 3.13 Mn OD1 B:Asp349 2.05 Mn CG B:Asp349 3.04 Mn CA B:Asp349 3.54 Mn N B:Ala350 4.31 Mn CA B:Ala350 4.72 Mn N B:Glu351 4.34 Mn OE1 B:Glu351 2.16 Mn CB B:Glu351 4.96 Mn OE2 B:Glu351 3.39 Mn CD B:Glu351 3.10 Mn CG B:Glu351 4.48 Mn ZN B:Zn501 3.28 Mn O1 B:Bct504 4.72 Mn O2 B:Bct504 4.00 Mn C B:Bct504 4.73 Mn N2 B:Bes505 4.22 Mn C1 B:Bes505 3.81 Mn O3 B:Bes505 2.41 Mn C2 B:Bes505 3.09 Mn N1 B:Bes505 4.11 Mn O2 B:Bes505 2.15 Mn C4 B:Bes505 4.82 Mn C3 B:Bes505 2.96 interactive model: Manganese binding site 3 out of 6 in 3h8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3h8g. 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: Asp272, C: Gly274, C: Lys279, C: Asp290, C: Asn322, C: Asp349, C: Ala350, C: Glu351, C: Zn501, C: Bct504, C: Bes505, conact list: Atom Atom Distance (A) Mn CB C:Asp272 4.46 Mn OD2 C:Asp272 2.15 Mn OD1 C:Asp272 3.20 Mn CG C:Asp272 3.00 Mn CA C:Gly274 4.87 Mn CE C:Lys279 4.12 Mn NZ C:Lys279 3.84 Mn OD2 C:Asp290 4.90 Mn ND2 C:Asn322 4.69 Mn O C:Asp349 2.15 Mn N C:Asp349 4.91 Mn CB C:Asp349 3.81 Mn OD2 C:Asp349 3.92 Mn C C:Asp349 3.08 Mn OD1 C:Asp349 2.07 Mn CG C:Asp349 3.04 Mn CA C:Asp349 3.49 Mn N C:Ala350 4.27 Mn CA C:Ala350 4.69 Mn N C:Glu351 4.34 Mn OE1 C:Glu351 2.09 Mn CB C:Glu351 4.96 Mn OE2 C:Glu351 3.37 Mn CD C:Glu351 3.08 Mn CG C:Glu351 4.47 Mn ZN C:Zn501 3.27 Mn O1 C:Bct504 4.01 Mn C C:Bct504 4.77 Mn O3 C:Bct504 4.76 Mn N2 C:Bes505 4.23 Mn C1 C:Bes505 3.84 Mn O3 C:Bes505 2.46 Mn C2 C:Bes505 3.09 Mn N1 C:Bes505 4.13 Mn O2 C:Bes505 2.17 Mn C4 C:Bes505 4.83 Mn C3 C:Bes505 2.97 interactive model: Manganese binding site 4 out of 6 in 3h8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3h8g. 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: Asp272, D: Gly274, D: Lys279, D: Asp290, D: Asn322, D: Asp349, D: Ala350, D: Glu351, D: Zn501, D: Bct504, D: Bes505, conact list: Atom Atom Distance (A) Mn CB D:Asp272 4.48 Mn OD2 D:Asp272 2.18 Mn OD1 D:Asp272 3.26 Mn CG D:Asp272 3.06 Mn CA D:Gly274 4.87 Mn CE D:Lys279 4.07 Mn NZ D:Lys279 3.81 Mn OD2 D:Asp290 4.88 Mn ND2 D:Asn322 4.73 Mn O D:Asp349 2.20 Mn N D:Asp349 4.93 Mn CB D:Asp349 3.84 Mn OD2 D:Asp349 3.93 Mn C D:Asp349 3.12 Mn OD1 D:Asp349 2.10 Mn CG D:Asp349 3.08 Mn CA D:Asp349 3.52 Mn N D:Ala350 4.29 Mn CA D:Ala350 4.70 Mn N D:Glu351 4.35 Mn OE1 D:Glu351 2.15 Mn CB D:Glu351 4.97 Mn OE2 D:Glu351 3.37 Mn CD D:Glu351 3.12 Mn CG D:Glu351 4.50 Mn ZN D:Zn501 3.28 Mn O1 D:Bct504 4.76 Mn C D:Bct504 4.77 Mn O3 D:Bct504 3.98 Mn N2 D:Bes505 4.21 Mn C1 D:Bes505 3.76 Mn O3 D:Bes505 2.45 Mn C2 D:Bes505 3.06 Mn N1 D:Bes505 4.11 Mn O2 D:Bes505 2.19 Mn C4 D:Bes505 4.79 Mn C3 D:Bes505 2.96 interactive model: Manganese binding site 5 out of 6 in 3h8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3h8g. 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: Asp272, E: Gly274, E: Lys279, E: Asp290, E: Asn322, E: Asp349, E: Ala350, E: Glu351, E: Zn501, E: Bct504, E: Bes505, conact list: Atom Atom Distance (A) Mn CB E:Asp272 4.45 Mn OD2 E:Asp272 2.19 Mn OD1 E:Asp272 3.22 Mn CG E:Asp272 3.04 Mn CA E:Gly274 4.87 Mn CE E:Lys279 4.05 Mn NZ E:Lys279 3.82 Mn OD2 E:Asp290 4.92 Mn ND2 E:Asn322 4.72 Mn O E:Asp349 2.17 Mn N E:Asp349 4.91 Mn CB E:Asp349 3.83 Mn OD2 E:Asp349 3.92 Mn C E:Asp349 3.10 Mn OD1 E:Asp349 2.10 Mn CG E:Asp349 3.06 Mn CA E:Asp349 3.51 Mn N E:Ala350 4.28 Mn CA E:Ala350 4.71 Mn N E:Glu351 4.33 Mn OE1 E:Glu351 2.14 Mn CB E:Glu351 4.96 Mn OE2 E:Glu351 3.41 Mn CD E:Glu351 3.13 Mn CG E:Glu351 4.51 Mn ZN E:Zn501 3.28 Mn O2 E:Bct504 4.74 Mn C E:Bct504 4.73 Mn O3 E:Bct504 3.96 Mn N2 E:Bes505 4.19 Mn C1 E:Bes505 3.78 Mn O3 E:Bes505 2.39 Mn C2 E:Bes505 3.07 Mn N1 E:Bes505 4.11 Mn O2 E:Bes505 2.15 Mn C4 E:Bes505 4.78 Mn C3 E:Bes505 2.97 interactive model: Manganese binding site 6 out of 6 in 3h8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3h8g. 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: Asp272, F: Gly274, F: Lys279, F: Asp290, F: Asn322, F: Asp349, F: Ala350, F: Glu351, F: Zn501, F: Bct504, F: Bes505, conact list: Atom Atom Distance (A) Mn CB F:Asp272 4.45 Mn OD2 F:Asp272 2.15 Mn OD1 F:Asp272 3.23 Mn CG F:Asp272 3.04 Mn CA F:Gly274 4.89 Mn CE F:Lys279 4.10 Mn NZ F:Lys279 3.84 Mn OD2 F:Asp290 4.91 Mn ND2 F:Asn322 4.69 Mn O F:Asp349 2.20 Mn N F:Asp349 4.93 Mn CB F:Asp349 3.85 Mn OD2 F:Asp349 3.93 Mn C F:Asp349 3.13 Mn OD1 F:Asp349 2.13 Mn CG F:Asp349 3.07 Mn CA F:Asp349 3.54 Mn N F:Ala350 4.30 Mn CA F:Ala350 4.73 Mn N F:Glu351 4.34 Mn OE1 F:Glu351 2.14 Mn CB F:Glu351 4.95 Mn OE2 F:Glu351 3.38 Mn CD F:Glu351 3.08 Mn CG F:Glu351 4.45 Mn ZN F:Zn501 3.27 Mn O2 F:Bct504 3.99 Mn C F:Bct504 4.73 Mn O3 F:Bct504 4.75 Mn N2 F:Bes505 4.22 Mn C1 F:Bes505 3.79 Mn O3 F:Bes505 2.45 Mn C2 F:Bes505 3.05 Mn N1 F:Bes505 4.12 Mn O2 F:Bes505 2.11 Mn C4 F:Bes505 4.80 Mn C3 F:Bes505 2.97 interactive model: