Manganese in the structure of P4 Protein From Bacteriophage PHI12 in Complex With Adp and Mn (pdb 1w47)

The binding sites of Manganese atom in the structure of P4 Protein From Bacteriophage PHI12 in Complex With Adp and Mn (pdb code 1w47). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1w47 structure was solved by E.J.MANCINI, D.E.KAINOV, J.M.GRIMES, R.TUMA, D.H.BAMFORD, D.I.STUART, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.5 Space group I222 a (A) 104.800 b (A) 128.200 c (A) 158.400 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.92 Rfree (%) 19.85 Manganese Binding Sites: Manganese binding site 1 out of 3 in 1w47 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1w47. 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: Thr137, A: Glu160, A: Asp189, A: Ser232, A: Adp700, A: Hoh2113, A: Hoh2115, conact list: Atom Atom Distance (A) Mn N A:Thr137 4.33 Mn CB A:Thr137 3.90 Mn OG1 A:Thr137 2.73 Mn CA A:Thr137 4.51 Mn OE2 A:Glu160 4.30 Mn CD A:Glu160 4.72 Mn OD2 A:Asp189 4.87 Mn OD1 A:Asp189 3.51 Mn CG A:Asp189 4.58 Mn CB A:Ser232 4.72 Mn OG A:Ser232 3.75 Mn O3B A:Adp700 4.77 Mn PA A:Adp700 4.07 Mn O2A A:Adp700 3.00 Mn O1B A:Adp700 2.36 Mn PB A:Adp700 3.72 Mn O2B A:Adp700 4.37 Mn O3A A:Adp700 4.23 Mn O1A A:Adp700 4.59 Mn O A:Hoh2113 3.37 Mn O A:Hoh2115 3.93 interactive model: Manganese binding site 2 out of 3 in 1w47 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1w47. 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: Arg272, B: Thr137, B: Glu160, B: Asp189, B: Ser232, B: Adp700, A: Hoh2148, B: Hoh2100, B: Hoh2103, conact list: Atom Atom Distance (A) Mn NH2 A:Arg272 4.97 Mn N B:Thr137 4.33 Mn CB B:Thr137 3.88 Mn OG1 B:Thr137 2.72 Mn CA B:Thr137 4.51 Mn OE2 B:Glu160 4.31 Mn CD B:Glu160 4.72 Mn OD2 B:Asp189 4.86 Mn OD1 B:Asp189 3.52 Mn CG B:Asp189 4.57 Mn CB B:Ser232 4.74 Mn OG B:Ser232 3.77 Mn O3B B:Adp700 4.76 Mn PA B:Adp700 4.06 Mn O2A B:Adp700 2.99 Mn O1B B:Adp700 2.35 Mn PB B:Adp700 3.71 Mn O2B B:Adp700 4.36 Mn O3A B:Adp700 4.21 Mn O1A B:Adp700 4.58 Mn O A:Hoh2148 3.90 Mn O B:Hoh2100 3.42 Mn O B:Hoh2103 4.14 interactive model: Manganese binding site 3 out of 3 in 1w47 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1w47. 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: Thr137, C: Glu160, C: Asp189, C: Ser232, C: Adp700, C: Hoh2112, C: Hoh2164, conact list: Atom Atom Distance (A) Mn N C:Thr137 4.32 Mn CB C:Thr137 3.87 Mn OG1 C:Thr137 2.70 Mn CA C:Thr137 4.50 Mn OE2 C:Glu160 4.31 Mn CD C:Glu160 4.72 Mn OD2 C:Asp189 4.89 Mn OD1 C:Asp189 3.52 Mn CG C:Asp189 4.59 Mn CB C:Ser232 4.76 Mn OG C:Ser232 3.78 Mn O3B C:Adp700 4.75 Mn PA C:Adp700 4.05 Mn O2A C:Adp700 2.97 Mn O1B C:Adp700 2.34 Mn PB C:Adp700 3.71 Mn O2B C:Adp700 4.36 Mn O3A C:Adp700 4.20 Mn O1A C:Adp700 4.56 Mn O C:Hoh2112 4.02 Mn O C:Hoh2164 4.10 interactive model: