Manganese in the structure of Crystal Structure of Human Arginase I in Complex With 2- Aminohomohistidine (pdb 3mfv)

The binding sites of Manganese atom in the structure of Crystal Structure of Human Arginase I in Complex With 2- Aminohomohistidine (pdb code 3mfv). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3mfv structure was solved by L.DI COSTANZO, D.W.CHRISTIANSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.9 Space group P3 a (A) 90.660 b (A) 90.660 c (A) 69.707 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 14.1 Rfree (%) 19 Manganese Binding Sites: Manganese binding site 1 out of 4 in 3mfv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3mfv. 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: Thr246, A: Mn615, A: Z700, A: Hoh400, conact list: Atom Atom Distance (A) Mn CB A:Asp124 4.31 Mn OD2 A:Asp124 3.25 Mn C A:Asp124 4.71 Mn OD1 A:Asp124 2.03 Mn CG A:Asp124 2.96 Mn CA A:Asp124 4.65 Mn N A:Ala125 3.90 Mn C A:Ala125 4.63 Mn CB A:Ala125 4.47 Mn CA A:Ala125 4.58 Mn NE2 A:His126 4.08 Mn N A:His126 3.90 Mn CB A:His126 3.96 Mn ND1 A:His126 2.17 Mn CD2 A:His126 4.36 Mn CE1 A:His126 2.84 Mn CG A:His126 3.40 Mn CA A:His126 4.55 Mn OD2 A:Asp128 4.98 Mn OD1 A:Asp128 4.77 Mn CB A:Asp232 4.15 Mn OD2 A:Asp232 2.15 Mn OD1 A:Asp232 3.88 Mn CG A:Asp232 3.19 Mn CB A:Asp234 4.18 Mn OD2 A:Asp234 2.31 Mn C A:Asp234 4.99 Mn OD1 A:Asp234 2.35 Mn CG A:Asp234 2.66 Mn OG1 A:Thr246 4.27 Mn MN A:Mn615 3.45 Mn C5 A:Z700 4.44 Mn N3 A:Z700 3.42 Mn N2 A:Z700 4.12 Mn C4 A:Z700 3.21 Mn C3 A:Z700 4.76 Mn N4 A:Z700 2.86 Mn O A:Hoh400 4.81 interactive model: Manganese binding site 2 out of 4 in 3mfv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3mfv. 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: His126, A: Asp128, A: His141, A: Asp232, A: Glu277, A: Mn614, A: Z700, conact list: Atom Atom Distance (A) Mn NE2 A:His101 4.39 Mn CB A:His101 3.38 Mn ND1 A:His101 2.30 Mn CD2 A:His101 4.36 Mn CE1 A:His101 3.31 Mn CG A:His101 3.19 Mn CA A:His101 4.90 Mn CZ2 A:Trp122 4.57 Mn CE2 A:Trp122 4.82 Mn NE1 A:Trp122 4.35 Mn CB A:Asp124 4.37 Mn OD2 A:Asp124 2.02 Mn OD1 A:Asp124 3.55 Mn CG A:Asp124 3.11 Mn ND1 A:His126 4.88 Mn CB A:Asp128 4.40 Mn OD2 A:Asp128 2.13 Mn OD1 A:Asp128 3.48 Mn CG A:Asp128 3.11 Mn O A:His141 4.21 Mn CB A:Asp232 3.74 Mn OD2 A:Asp232 2.58 Mn OD1 A:Asp232 4.47 Mn CG A:Asp232 3.43 Mn OE2 A:Glu277 4.49 Mn CG A:Glu277 4.67 Mn MN A:Mn614 3.45 Mn N3 A:Z700 4.62 Mn N2 A:Z700 3.74 Mn C4 A:Z700 3.38 Mn N4 A:Z700 2.35 interactive model: Manganese binding site 3 out of 4 in 3mfv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3mfv. 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: Thr246, B: Glu277, B: Mn615, B: Z70323, B: Hoh331, conact list: Atom Atom Distance (A) Mn CB B:Asp124 4.50 Mn OD2 B:Asp124 3.22 Mn OD1 B:Asp124 2.27 Mn CG B:Asp124 3.08 Mn CA B:Asp124 4.94 Mn N B:Ala125 4.31 Mn C B:Ala125 4.96 Mn CB B:Ala125 4.91 Mn NE2 B:His126 4.22 Mn N B:His126 4.12 Mn CB B:His126 3.90 Mn ND1 B:His126 2.26 Mn CD2 B:His126 4.43 Mn CE1 B:His126 3.01 Mn CG B:His126 3.41 Mn CA B:His126 4.63 Mn OD2 B:Asp128 4.86 Mn OD1 B:Asp128 4.71 Mn CB B:Asp232 3.97 Mn OD2 B:Asp232 2.11 Mn OD1 B:Asp232 3.55 Mn CG B:Asp232 2.98 Mn CB B:Asp234 4.06 Mn OD2 B:Asp234 2.40 Mn C B:Asp234 4.99 Mn OD1 B:Asp234 2.08 Mn CG B:Asp234 2.55 Mn CA B:Asp234 4.98 Mn OG1 B:Thr246 4.40 Mn CG B:Glu277 4.99 Mn MN B:Mn615 3.39 Mn C5 B:Z70323 4.36 Mn N3 B:Z70323 3.32 Mn N2 B:Z70323 4.01 Mn C4 B:Z70323 3.07 Mn C3 B:Z70323 4.68 Mn N4 B:Z70323 2.69 Mn O B:Hoh331 4.85 interactive model: Manganese binding site 4 out of 4 in 3mfv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3mfv. 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: Mn614, B: Z70323, conact list: Atom Atom Distance (A) Mn NE2 B:His101 4.47 Mn CB B:His101 3.27 Mn ND1 B:His101 2.37 Mn CD2 B:His101 4.37 Mn CE1 B:His101 3.43 Mn CG B:His101 3.17 Mn CA B:His101 4.80 Mn CZ2 B:Trp122 4.32 Mn CE2 B:Trp122 4.65 Mn NE1 B:Trp122 4.27 Mn CB B:Asp124 4.64 Mn OD2 B:Asp124 2.29 Mn OD1 B:Asp124 3.82 Mn CG B:Asp124 3.39 Mn CB B:Asp128 4.37 Mn OD2 B:Asp128 2.08 Mn OD1 B:Asp128 3.49 Mn CG B:Asp128 3.08 Mn O B:His141 4.15 Mn CB B:Asp232 3.82 Mn OD2 B:Asp232 2.64 Mn OD1 B:Asp232 4.73 Mn CG B:Asp232 3.59 Mn OE2 B:Glu277 4.88 Mn CG B:Glu277 4.75 Mn MN B:Mn614 3.39 Mn N3 B:Z70323 4.76 Mn N2 B:Z70323 3.77 Mn C4 B:Z70323 3.50 Mn N4 B:Z70323 2.57 interactive model: