Manganese in the structure of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex (pdb 3e8z)

The binding sites of Manganese atom in the structure of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex (pdb code 3e8z). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3e8z structure was solved by E.Y.SHISHOVA, L.DI COSTANZO, D.W.CHRISTIANSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 41.8-2.0 Space group P32 a (A) 87.500 b (A) 87.500 c (A) 100.110 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.6 Rfree (%) 28 Manganese Binding Sites: Manganese binding site 1 out of 6 in 3e8z Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3e8z. 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: Hoh599, conact list: Atom Atom Distance (A) Mn NE2 A:His101 4.50 Mn CB A:His101 3.42 Mn ND1 A:His101 2.38 Mn CD2 A:His101 4.45 Mn CE1 A:His101 3.41 Mn CG A:His101 3.27 Mn CA A:His101 4.95 Mn CZ2 A:Trp122 4.51 Mn CE2 A:Trp122 4.77 Mn NE1 A:Trp122 4.34 Mn CB A:Asp124 4.48 Mn OD2 A:Asp124 2.13 Mn OD1 A:Asp124 3.54 Mn CG A:Asp124 3.17 Mn CB A:Asp128 4.48 Mn OD2 A:Asp128 2.20 Mn OD1 A:Asp128 3.35 Mn CG A:Asp128 3.12 Mn O A:His141 4.47 Mn CB A:Asp232 3.63 Mn OD2 A:Asp232 2.24 Mn OD1 A:Asp232 4.38 Mn CG A:Asp232 3.26 Mn CA A:Asp232 4.96 Mn OE2 A:Glu277 4.79 Mn CG A:Glu277 4.73 Mn MN A:Mn501 3.35 Mn O A:Hoh599 2.62 interactive model: Manganese binding site 2 out of 6 in 3e8z Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3e8z. 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: Hoh537, A: Hoh599, conact list: Atom Atom Distance (A) Mn CB A:Asp124 4.56 Mn OD2 A:Asp124 3.40 Mn OD1 A:Asp124 2.23 Mn CG A:Asp124 3.16 Mn CA A:Asp124 4.99 Mn N A:Ala125 4.28 Mn C A:Ala125 4.89 Mn CB A:Ala125 4.70 Mn CA A:Ala125 4.93 Mn NE2 A:His126 4.25 Mn N A:His126 4.02 Mn CB A:His126 3.71 Mn ND1 A:His126 2.37 Mn CD2 A:His126 4.33 Mn CE1 A:His126 3.18 Mn CG A:His126 3.31 Mn CA A:His126 4.50 Mn OD2 A:Asp128 4.91 Mn OD1 A:Asp128 4.56 Mn CB A:Asp232 4.19 Mn OD2 A:Asp232 2.68 Mn OD1 A:Asp232 3.55 Mn CG A:Asp232 3.21 Mn CB A:Asp234 4.21 Mn OD2 A:Asp234 2.17 Mn OD1 A:Asp234 2.58 Mn CG A:Asp234 2.70 Mn MN A:Mn500 3.35 Mn O A:Hoh537 4.53 Mn O A:Hoh599 2.34 interactive model: Manganese binding site 3 out of 6 in 3e8z Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3e8z. 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: Mn501, B: Hoh587, conact list: Atom Atom Distance (A) Mn NE2 B:His101 4.34 Mn CB B:His101 3.36 Mn ND1 B:His101 2.24 Mn CD2 B:His101 4.32 Mn CE1 B:His101 3.26 Mn CG B:His101 3.15 Mn CA B:His101 4.89 Mn CZ2 B:Trp122 4.62 Mn CE2 B:Trp122 4.85 Mn NE1 B:Trp122 4.40 Mn CB B:Asp124 4.46 Mn OD2 B:Asp124 2.12 Mn OD1 B:Asp124 3.62 Mn CG B:Asp124 3.20 Mn CB B:Asp128 4.51 Mn OD2 B:Asp128 2.20 Mn OD1 B:Asp128 3.42 Mn CG B:Asp128 3.15 Mn O B:His141 4.57 Mn CB B:Asp232 3.59 Mn OD2 B:Asp232 2.31 Mn OD1 B:Asp232 4.42 Mn CG B:Asp232 3.29 Mn CA B:Asp232 4.93 Mn CG B:Glu277 4.80 Mn MN B:Mn501 3.27 Mn O B:Hoh587 2.25 interactive model: Manganese binding site 4 out of 6 in 3e8z Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3e8z. 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: Mn500, B: Hoh531, B: Hoh555, B: Hoh587, conact list: Atom Atom Distance (A) Mn CB B:Asp124 4.51 Mn OD2 B:Asp124 3.27 Mn OD1 B:Asp124 2.26 Mn CG B:Asp124 3.11 Mn CA B:Asp124 4.95 Mn N B:Ala125 4.37 Mn C B:Ala125 4.98 Mn NE2 B:His126 4.33 Mn N B:His126 4.13 Mn CB B:His126 3.83 Mn ND1 B:His126 2.32 Mn CD2 B:His126 4.48 Mn CE1 B:His126 3.13 Mn CG B:His126 3.42 Mn CA B:His126 4.59 Mn OD2 B:Asp128 4.71 Mn OD1 B:Asp128 4.38 Mn CG B:Asp128 4.99 Mn CB B:Asp232 4.18 Mn OD2 B:Asp232 2.35 Mn OD1 B:Asp232 3.78 Mn CG B:Asp232 3.21 Mn CB B:Asp234 4.31 Mn OD2 B:Asp234 2.28 Mn OD1 B:Asp234 2.69 Mn CG B:Asp234 2.82 Mn MN B:Mn500 3.27 Mn O B:Hoh531 4.56 Mn O B:Hoh555 4.81 Mn O B:Hoh587 2.32 interactive model: Manganese binding site 5 out of 6 in 3e8z Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3e8z. 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: His101, C: Trp122, C: Asp124, C: His126, C: Asp128, C: His141, C: Asp232, C: Asp234, C: Glu277, C: Mn501, C: Hoh555, conact list: Atom Atom Distance (A) Mn NE2 C:His101 4.48 Mn CB C:His101 3.35 Mn ND1 C:His101 2.35 Mn CD2 C:His101 4.41 Mn CE1 C:His101 3.40 Mn CG C:His101 3.22 Mn CA C:His101 4.86 Mn CZ2 C:Trp122 4.81 Mn CE2 C:Trp122 4.96 Mn NE1 C:Trp122 4.45 Mn CB C:Asp124 4.48 Mn OD2 C:Asp124 2.25 Mn OD1 C:Asp124 3.68 Mn CG C:Asp124 3.26 Mn ND1 C:His126 4.92 Mn CB C:Asp128 4.55 Mn OD2 C:Asp128 2.28 Mn OD1 C:Asp128 3.61 Mn CG C:Asp128 3.26 Mn O C:His141 4.54 Mn CB C:Asp232 3.56 Mn OD2 C:Asp232 2.28 Mn OD1 C:Asp232 4.40 Mn CG C:Asp232 3.26 Mn CA C:Asp232 4.91 Mn OD2 C:Asp234 4.81 Mn OE2 C:Glu277 4.86 Mn CG C:Glu277 4.53 Mn MN C:Mn501 3.33 Mn O C:Hoh555 2.48 interactive model: Manganese binding site 6 out of 6 in 3e8z Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3e8z. 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: Asp124, C: Ala125, C: His126, C: Asp128, C: Asp232, C: Asp234, C: Mn500, C: Hoh525, C: Hoh555, conact list: Atom Atom Distance (A) Mn CB C:Asp124 4.53 Mn OD2 C:Asp124 3.35 Mn OD1 C:Asp124 2.28 Mn CG C:Asp124 3.14 Mn CA C:Asp124 4.87 Mn N C:Ala125 4.17 Mn C C:Ala125 4.85 Mn CB C:Ala125 4.74 Mn CA C:Ala125 4.87 Mn NE2 C:His126 4.05 Mn N C:His126 4.04 Mn CB C:His126 3.87 Mn ND1 C:His126 2.15 Mn CD2 C:His126 4.30 Mn CE1 C:His126 2.85 Mn CG C:His126 3.33 Mn CA C:His126 4.58 Mn OD2 C:Asp128 4.82 Mn OD1 C:Asp128 4.53 Mn CB C:Asp232 4.17 Mn OD2 C:Asp232 2.49 Mn OD1 C:Asp232 3.75 Mn CG C:Asp232 3.23 Mn CB C:Asp234 4.06 Mn OD2 C:Asp234 2.03 Mn OD1 C:Asp234 2.46 Mn CG C:Asp234 2.56 Mn CA C:Asp234 4.99 Mn MN C:Mn500 3.33 Mn O C:Hoh525 4.48 Mn O C:Hoh555 2.47 interactive model: