Manganese in the structure of Crystal Structure Of The Complex Between Calyculin A and the Catalytic Subunit of Protein Phosphatase 1 (pdb 1it6)

The binding sites of Manganese atom in the structure of Crystal Structure Of The Complex Between Calyculin A and the Catalytic Subunit of Protein Phosphatase 1 (pdb code 1it6). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1it6 structure was solved by A.KITA, S.MATSUNAGA, A.TAKAI, H.KATAIWA, T.WAKIMOTO, N.FUSETANI, M.ISOBE, K.MIKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.0 Space group P21212 a (A) 98.090 b (A) 136.360 c (A) 61.580 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.2 Rfree (%) 21.8 Manganese Binding Sites: Manganese binding site 1 out of 4 in 1it6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1it6. 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: Asp64, A: His66, A: Asp92, A: Asn124, A: His125, A: His173, A: His248, A: Phe267, A: Tyr272, A: Mn402, A: Cyu501, A: Hoh601, A: Hoh602, A: Hoh612, conact list: Atom Atom Distance (A) Mn CB A:Asp64 4.01 Mn OD2 A:Asp64 4.20 Mn OD1 A:Asp64 2.36 Mn CG A:Asp64 3.34 Mn NE2 A:His66 2.31 Mn ND1 A:His66 4.44 Mn CD2 A:His66 3.28 Mn CE1 A:His66 3.31 Mn CG A:His66 4.45 Mn CB A:Asp92 3.84 Mn OD2 A:Asp92 2.40 Mn OD1 A:Asp92 4.54 Mn CG A:Asp92 3.45 Mn OD1 A:Asn124 4.72 Mn NE2 A:His125 4.46 Mn CD2 A:His125 4.27 Mn NE2 A:His173 4.62 Mn CE1 A:His173 4.80 Mn O A:His248 3.79 Mn ND1 A:His248 4.95 Mn C A:His248 4.45 Mn CA A:His248 4.45 Mn CZ A:Phe267 4.77 Mn CE1 A:Phe267 4.30 Mn OH A:Tyr272 4.38 Mn MN A:Mn402 3.28 Mn O6 A:Cyu501 4.15 Mn O A:Hoh601 2.33 Mn O A:Hoh602 2.28 Mn O A:Hoh612 4.07 interactive model: Manganese binding site 2 out of 4 in 1it6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1it6. 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: Asp64, A: Asp92, A: Asn124, A: His125, A: His173, A: Leu205, A: His248, A: Mn401, A: Hoh601, A: Hoh602, A: Hoh612, conact list: Atom Atom Distance (A) Mn OD2 A:Asp64 5.00 Mn OD1 A:Asp64 4.20 Mn CG A:Asp64 4.94 Mn CB A:Asp92 4.58 Mn OD2 A:Asp92 2.50 Mn OD1 A:Asp92 3.67 Mn CG A:Asp92 3.35 Mn N A:Asn124 4.34 Mn CB A:Asn124 4.30 Mn ND2 A:Asn124 3.78 Mn OD1 A:Asn124 2.28 Mn CG A:Asn124 3.20 Mn CA A:Asn124 4.86 Mn NE2 A:His125 4.82 Mn CD2 A:His125 4.19 Mn NE2 A:His173 2.33 Mn ND1 A:His173 4.46 Mn CD2 A:His173 3.25 Mn CE1 A:His173 3.35 Mn CG A:His173 4.44 Mn O A:Leu205 4.57 Mn O A:His248 3.91 Mn NE2 A:His248 4.45 Mn N A:His248 4.54 Mn CB A:His248 3.77 Mn ND1 A:His248 2.37 Mn CD2 A:His248 4.55 Mn C A:His248 4.24 Mn CE1 A:His248 3.25 Mn CG A:His248 3.43 Mn CA A:His248 3.56 Mn MN A:Mn401 3.28 Mn O A:Hoh601 2.29 Mn O A:Hoh602 4.92 Mn O A:Hoh612 3.62 interactive model: Manganese binding site 3 out of 4 in 1it6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1it6. 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: Asp64, B: His66, B: Asp92, B: Asn124, B: His125, B: His173, B: His248, B: Phe267, B: Tyr272, B: Mn402, B: Cyu1501, B: Hoh603, B: Hoh604, B: Hoh615, conact list: Atom Atom Distance (A) Mn CB B:Asp64 4.10 Mn OD2 B:Asp64 2.37 Mn OD1 B:Asp64 4.25 Mn CG B:Asp64 3.39 Mn NE2 B:His66 2.37 Mn ND1 B:His66 4.54 Mn CD2 B:His66 3.28 Mn CE1 B:His66 3.45 Mn CG B:His66 4.49 Mn CB B:Asp92 3.97 Mn OD2 B:Asp92 2.38 Mn OD1 B:Asp92 4.55 Mn CG B:Asp92 3.49 Mn OD1 B:Asn124 4.69 Mn NE2 B:His125 4.49 Mn CD2 B:His125 4.33 Mn NE2 B:His173 4.54 Mn CE1 B:His173 4.81 Mn O B:His248 3.77 Mn ND1 B:His248 4.76 Mn C B:His248 4.40 Mn CA B:His248 4.36 Mn CE1 B:Phe267 4.37 Mn OH B:Tyr272 4.41 Mn MN B:Mn402 3.09 Mn O6 B:Cyu1501 3.99 Mn O B:Hoh603 2.34 Mn O B:Hoh604 2.30 Mn O B:Hoh615 3.83 interactive model: Manganese binding site 4 out of 4 in 1it6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1it6. 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: Asp64, B: His66, B: Asp92, B: Asn124, B: His125, B: His173, B: Leu205, B: His248, B: Mn401, B: Hoh603, B: Hoh604, B: Hoh615, conact list: Atom Atom Distance (A) Mn OD2 B:Asp64 4.07 Mn OD1 B:Asp64 4.94 Mn CG B:Asp64 4.83 Mn NE2 B:His66 4.92 Mn CB B:Asp92 4.58 Mn OD2 B:Asp92 2.42 Mn OD1 B:Asp92 3.67 Mn CG B:Asp92 3.33 Mn N B:Asn124 4.39 Mn CB B:Asn124 4.45 Mn ND2 B:Asn124 3.71 Mn OD1 B:Asn124 2.30 Mn CG B:Asn124 3.24 Mn CA B:Asn124 4.96 Mn NE2 B:His125 4.86 Mn CD2 B:His125 4.23 Mn NE2 B:His173 2.35 Mn ND1 B:His173 4.48 Mn CD2 B:His173 3.26 Mn CE1 B:His173 3.37 Mn CG B:His173 4.45 Mn O B:Leu205 4.68 Mn O B:His248 3.93 Mn NE2 B:His248 4.48 Mn N B:His248 4.52 Mn CB B:His248 3.71 Mn ND1 B:His248 2.37 Mn CD2 B:His248 4.55 Mn C B:His248 4.25 Mn CE1 B:His248 3.29 Mn CG B:His248 3.42 Mn CA B:His248 3.54 Mn MN B:Mn401 3.09 Mn O B:Hoh603 2.33 Mn O B:Hoh604 4.84 Mn O B:Hoh615 3.54 interactive model: