Manganese in the structure of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed With 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog (pdb 1d3v)

The binding sites of Manganese atom in the structure of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed With 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog (pdb code 1d3v). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1d3v structure was solved by J.D.COX, N.N.KIM, A.M.TRAISH, D.W.CHRISTIANSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.7 Space group P3 a (A) 91.300 b (A) 91.300 c (A) 69.900 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 15.7 Rfree (%) 17.9 Manganese Binding Sites: Manganese binding site 1 out of 4 in 1d3v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1d3v. 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: His101, A: Trp122, A: Asp124, A: Asp128, A: His141, A: Asp232, A: Glu277, A: Mn501, A: Abh551, conact list: Atom Atom Distance (A) Mn NE2 A:His101 4.30 Mn CB A:His101 3.54 Mn ND1 A:His101 2.16 Mn CD2 A:His101 4.34 Mn CE1 A:His101 3.12 Mn CG A:His101 3.21 Mn CZ2 A:Trp122 4.62 Mn CE2 A:Trp122 4.82 Mn NE1 A:Trp122 4.34 Mn CB A:Asp124 4.47 Mn OD2 A:Asp124 2.13 Mn OD1 A:Asp124 3.51 Mn CG A:Asp124 3.16 Mn CB A:Asp128 4.55 Mn OD2 A:Asp128 2.22 Mn OD1 A:Asp128 3.52 Mn CG A:Asp128 3.21 Mn O A:His141 4.48 Mn CB A:Asp232 3.61 Mn OD2 A:Asp232 2.43 Mn OD1 A:Asp232 4.48 Mn CG A:Asp232 3.34 Mn CA A:Asp232 4.96 Mn CG A:Glu277 4.83 Mn MN A:Mn501 3.39 Mn O2 A:Abh551 2.36 Mn CE A:Abh551 4.09 Mn B A:Abh551 2.82 Mn O1 A:Abh551 2.20 Mn O3 A:Abh551 3.59 interactive model: Manganese binding site 2 out of 4 in 1d3v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1d3v. 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: Asp124, A: Ala125, A: His126, A: Asp128, A: Asp232, A: Asp234, A: Mn500, A: Abh551, A: Hoh555, A: Hoh645, conact list: Atom Atom Distance (A) Mn CB A:Asp124 4.59 Mn OD2 A:Asp124 3.48 Mn OD1 A:Asp124 2.31 Mn CG A:Asp124 3.23 Mn CA A:Asp124 4.97 Mn N A:Ala125 4.31 Mn C A:Ala125 4.99 Mn CB A:Ala125 4.88 Mn NE2 A:His126 4.57 Mn N A:His126 4.19 Mn CB A:His126 3.92 Mn ND1 A:His126 2.49 Mn CD2 A:His126 4.68 Mn CE1 A:His126 3.35 Mn CG A:His126 3.57 Mn CA A:His126 4.68 Mn OD2 A:Asp128 4.87 Mn OD1 A:Asp128 4.65 Mn CB A:Asp232 4.22 Mn OD2 A:Asp232 2.30 Mn OD1 A:Asp232 3.84 Mn CG A:Asp232 3.23 Mn CB A:Asp234 4.24 Mn OD2 A:Asp234 2.17 Mn OD1 A:Asp234 2.59 Mn CG A:Asp234 2.73 Mn MN A:Mn500 3.39 Mn O2 A:Abh551 4.06 Mn CE A:Abh551 4.23 Mn B A:Abh551 3.12 Mn O1 A:Abh551 2.21 Mn CD A:Abh551 4.27 Mn O3 A:Abh551 2.90 Mn O A:Hoh555 4.58 Mn O A:Hoh645 5.00 interactive model: Manganese binding site 3 out of 4 in 1d3v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1d3v. 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: His101, B: Trp122, B: Asp124, B: Asp128, B: His141, B: Asp232, B: Glu277, B: Mn503, B: Abh552, conact list: Atom Atom Distance (A) Mn NE2 B:His101 4.36 Mn CB B:His101 3.54 Mn ND1 B:His101 2.23 Mn CD2 B:His101 4.39 Mn CE1 B:His101 3.20 Mn CG B:His101 3.24 Mn CZ2 B:Trp122 4.64 Mn CE2 B:Trp122 4.84 Mn NE1 B:Trp122 4.36 Mn CB B:Asp124 4.52 Mn OD2 B:Asp124 2.18 Mn OD1 B:Asp124 3.62 Mn CG B:Asp124 3.23 Mn CB B:Asp128 4.53 Mn OD2 B:Asp128 2.17 Mn OD1 B:Asp128 3.36 Mn CG B:Asp128 3.12 Mn O B:His141 4.43 Mn CB B:Asp232 3.65 Mn OD2 B:Asp232 2.34 Mn OD1 B:Asp232 4.41 Mn CG B:Asp232 3.31 Mn CA B:Asp232 5.00 Mn CG B:Glu277 4.89 Mn MN B:Mn503 3.40 Mn O2 B:Abh552 2.43 Mn CE B:Abh552 4.10 Mn B B:Abh552 2.86 Mn O1 B:Abh552 2.20 Mn O3 B:Abh552 3.67 interactive model: Manganese binding site 4 out of 4 in 1d3v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1d3v. 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: Asp124, B: Ala125, B: His126, B: Asp128, B: Asp232, B: Asp234, B: Mn502, B: Abh552, B: Hoh667, conact list: Atom Atom Distance (A) Mn CB B:Asp124 4.58 Mn OD2 B:Asp124 3.43 Mn OD1 B:Asp124 2.29 Mn CG B:Asp124 3.19 Mn CA B:Asp124 4.97 Mn N B:Ala125 4.21 Mn C B:Ala125 4.88 Mn CB B:Ala125 4.76 Mn CA B:Ala125 4.88 Mn NE2 B:His126 4.45 Mn N B:His126 4.09 Mn CB B:His126 3.89 Mn ND1 B:His126 2.38 Mn CD2 B:His126 4.58 Mn CE1 B:His126 3.22 Mn CG B:His126 3.49 Mn CA B:His126 4.61 Mn OD2 B:Asp128 4.91 Mn OD1 B:Asp128 4.56 Mn CB B:Asp232 4.28 Mn OD2 B:Asp232 2.33 Mn OD1 B:Asp232 3.80 Mn CG B:Asp232 3.25 Mn CB B:Asp234 4.17 Mn OD2 B:Asp234 2.57 Mn OD1 B:Asp234 2.09 Mn CG B:Asp234 2.67 Mn MN B:Mn502 3.40 Mn O2 B:Abh552 4.09 Mn CE B:Abh552 4.26 Mn B B:Abh552 3.15 Mn O1 B:Abh552 2.21 Mn CD B:Abh552 4.36 Mn O3 B:Abh552 2.96 Mn O B:Hoh667 4.58 interactive model: