Manganese in the structure of Arginase-L-Valine Complex (pdb 1t4s)

The binding sites of Manganese atom in the structure of Arginase-L-Valine Complex (pdb code 1t4s). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1t4s structure was solved by E.CAMA, S.PETHE, J.-L.BOUCHER, H.SHOUFA, F.A.EMIG, D.E.ASH, R.E.VIOLA, D.MANSUY, D.W.CHRISTIANSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.7-2.8 Space group P32 a (A) 87.800 b (A) 87.800 c (A) 110.500 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 25.8 Rfree (%) 29.2 Manganese Binding Sites: Manganese binding site 1 out of 6 in 1t4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1t4s. 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: Asp124, A: Ala125, A: His126, A: Asp128, A: Asp232, A: Asp234, A: Thr246, A: Mn501, A: Hoh729, conact list: Atom Atom Distance (A) Mn ND1 A:His101 4.98 Mn CB A:Asp124 4.24 Mn OD2 A:Asp124 2.83 Mn C A:Asp124 4.83 Mn OD1 A:Asp124 2.29 Mn CG A:Asp124 2.84 Mn CA A:Asp124 4.69 Mn N A:Ala125 4.01 Mn C A:Ala125 4.76 Mn CB A:Ala125 4.77 Mn CA A:Ala125 4.78 Mn NE2 A:His126 4.05 Mn N A:His126 3.97 Mn CB A:His126 3.90 Mn ND1 A:His126 2.13 Mn CD2 A:His126 4.31 Mn CE1 A:His126 2.82 Mn CG A:His126 3.34 Mn CA A:His126 4.54 Mn OD2 A:Asp128 4.44 Mn OD1 A:Asp128 4.23 Mn CG A:Asp128 4.79 Mn CB A:Asp232 4.03 Mn OD2 A:Asp232 2.28 Mn OD1 A:Asp232 3.67 Mn CG A:Asp232 3.07 Mn CB A:Asp234 4.21 Mn OD2 A:Asp234 2.25 Mn OD1 A:Asp234 2.48 Mn CG A:Asp234 2.69 Mn OG1 A:Thr246 4.61 Mn MN A:Mn501 3.11 Mn O A:Hoh729 2.67 interactive model: Manganese binding site 2 out of 6 in 1t4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1t4s. 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: Asp234, A: Glu277, A: Mn500, A: Hoh729, conact list: Atom Atom Distance (A) Mn NE2 A:His101 4.38 Mn CB A:His101 3.33 Mn ND1 A:His101 2.27 Mn CD2 A:His101 4.33 Mn CE1 A:His101 3.30 Mn CG A:His101 3.16 Mn CA A:His101 4.86 Mn CZ2 A:Trp122 4.65 Mn CE2 A:Trp122 4.97 Mn NE1 A:Trp122 4.55 Mn CB A:Asp124 4.42 Mn OD2 A:Asp124 2.13 Mn OD1 A:Asp124 3.89 Mn CG A:Asp124 3.29 Mn ND1 A:His126 4.70 Mn CB A:Asp128 4.33 Mn OD2 A:Asp128 2.15 Mn OD1 A:Asp128 3.26 Mn CG A:Asp128 3.00 Mn O A:His141 4.26 Mn CB A:Asp232 3.77 Mn OD2 A:Asp232 2.30 Mn OD1 A:Asp232 4.47 Mn CG A:Asp232 3.35 Mn OD2 A:Asp234 4.75 Mn OD1 A:Asp234 4.99 Mn OE2 A:Glu277 4.60 Mn CG A:Glu277 4.81 Mn MN A:Mn500 3.11 Mn O A:Hoh729 2.38 interactive model: Manganese binding site 3 out of 6 in 1t4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1t4s. 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: Mn503, B: Hoh726, B: Hoh730, conact list: Atom Atom Distance (A) Mn CB B:Asp124 4.25 Mn OD2 B:Asp124 2.87 Mn C B:Asp124 4.87 Mn OD1 B:Asp124 2.21 Mn CG B:Asp124 2.83 Mn CA B:Asp124 4.70 Mn N B:Ala125 4.06 Mn C B:Ala125 4.86 Mn CB B:Ala125 4.79 Mn CA B:Ala125 4.84 Mn NE2 B:His126 4.02 Mn N B:His126 4.02 Mn CB B:His126 3.87 Mn ND1 B:His126 2.10 Mn CD2 B:His126 4.28 Mn CE1 B:His126 2.79 Mn CG B:His126 3.31 Mn CA B:His126 4.55 Mn OD2 B:Asp128 4.48 Mn OD1 B:Asp128 4.29 Mn CG B:Asp128 4.84 Mn CB B:Asp232 4.00 Mn OD2 B:Asp232 2.13 Mn OD1 B:Asp232 3.63 Mn CG B:Asp232 3.01 Mn CB B:Asp234 4.19 Mn OD2 B:Asp234 2.21 Mn OD1 B:Asp234 2.46 Mn CG B:Asp234 2.66 Mn OG1 B:Thr246 4.51 Mn MN B:Mn503 3.11 Mn O B:Hoh726 4.50 Mn O B:Hoh730 2.72 interactive model: Manganese binding site 4 out of 6 in 1t4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1t4s. 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: His126, B: Asp128, B: His141, B: Asp232, B: Asp234, B: Glu277, B: Mn502, B: Hoh730, conact list: Atom Atom Distance (A) Mn NE2 B:His101 4.43 Mn CB B:His101 3.32 Mn ND1 B:His101 2.31 Mn CD2 B:His101 4.37 Mn CE1 B:His101 3.36 Mn CG B:His101 3.18 Mn CA B:His101 4.83 Mn CZ2 B:Trp122 4.68 Mn CE2 B:Trp122 4.98 Mn NE1 B:Trp122 4.56 Mn CB B:Asp124 4.43 Mn OD2 B:Asp124 2.13 Mn OD1 B:Asp124 3.83 Mn CG B:Asp124 3.27 Mn ND1 B:His126 4.65 Mn CB B:Asp128 4.37 Mn OD2 B:Asp128 2.20 Mn OD1 B:Asp128 3.32 Mn CG B:Asp128 3.05 Mn O B:His141 4.29 Mn CB B:Asp232 3.77 Mn OD2 B:Asp232 2.34 Mn OD1 B:Asp232 4.45 Mn CG B:Asp232 3.35 Mn OD2 B:Asp234 4.72 Mn OE2 B:Glu277 4.58 Mn CG B:Glu277 4.73 Mn MN B:Mn502 3.11 Mn O B:Hoh730 2.38 interactive model: Manganese binding site 5 out of 6 in 1t4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 1t4s. 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: Thr246, C: Mn505, C: Hoh728, conact list: Atom Atom Distance (A) Mn CB C:Asp124 4.24 Mn OD2 C:Asp124 2.86 Mn C C:Asp124 4.84 Mn OD1 C:Asp124 2.29 Mn CG C:Asp124 2.85 Mn CA C:Asp124 4.67 Mn N C:Ala125 4.03 Mn C C:Ala125 4.81 Mn CB C:Ala125 4.79 Mn CA C:Ala125 4.81 Mn NE2 C:His126 4.03 Mn N C:His126 4.01 Mn CB C:His126 3.95 Mn ND1 C:His126 2.13 Mn CD2 C:His126 4.32 Mn CE1 C:His126 2.79 Mn CG C:His126 3.36 Mn CA C:His126 4.58 Mn OD2 C:Asp128 4.53 Mn OD1 C:Asp128 4.31 Mn CG C:Asp128 4.87 Mn CB C:Asp232 4.03 Mn OD2 C:Asp232 2.24 Mn OD1 C:Asp232 3.62 Mn CG C:Asp232 3.05 Mn CB C:Asp234 4.17 Mn OD2 C:Asp234 2.15 Mn OD1 C:Asp234 2.50 Mn CG C:Asp234 2.65 Mn OG1 C:Thr246 4.51 Mn MN C:Mn505 3.12 Mn O C:Hoh728 2.78 interactive model: Manganese binding site 6 out of 6 in 1t4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 1t4s. 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: Mn504, C: Hoh728, conact list: Atom Atom Distance (A) Mn NE2 C:His101 4.43 Mn CB C:His101 3.34 Mn ND1 C:His101 2.30 Mn CD2 C:His101 4.37 Mn CE1 C:His101 3.35 Mn CG C:His101 3.18 Mn CA C:His101 4.86 Mn CZ2 C:Trp122 4.70 Mn CE2 C:Trp122 4.99 Mn NE1 C:Trp122 4.60 Mn CB C:Asp124 4.37 Mn OD2 C:Asp124 2.10 Mn OD1 C:Asp124 3.84 Mn CG C:Asp124 3.25 Mn ND1 C:His126 4.66 Mn CB C:Asp128 4.38 Mn OD2 C:Asp128 2.25 Mn OD1 C:Asp128 3.27 Mn CG C:Asp128 3.05 Mn O C:His141 4.28 Mn CB C:Asp232 3.79 Mn OD2 C:Asp232 2.28 Mn OD1 C:Asp232 4.44 Mn CG C:Asp232 3.34 Mn OD2 C:Asp234 4.84 Mn OD1 C:Asp234 4.97 Mn OE2 C:Glu277 4.70 Mn CG C:Glu277 4.77 Mn MN C:Mn504 3.12 Mn O C:Hoh728 2.28 interactive model: