Manganese in the structure of Crystal Structure Of Human Arginase I At 1.29 A Resolution and Exploration of Inhibition in Immune Response. (pdb 2aeb)

The binding sites of Manganese atom in the structure of Crystal Structure Of Human Arginase I At 1.29 A Resolution and Exploration of Inhibition in Immune Response. (pdb code 2aeb). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2aeb structure was solved by L.DI COSTANZO, G.SABIO, A.MORA, P.C.RODRIGUEZ, A.C.OCHOA, F.CENTENO, D.W.CHRISTIANSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 1.3 Space group P3 a (A) 91.422 b (A) 91.422 c (A) 69.637 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 16.5 Rfree (%) 17.9 Manganese Binding Sites: Manganese binding site 1 out of 4 in 2aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2aeb. 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: Glu277, A: Mn2363, A: Abh551, A: Hoh2391, A: Hoh2465, conact list: Atom Atom Distance (A) Mn CB A:Asp124 4.45 Mn HB3 A:Asp124 4.91 Mn HA A:Asp124 4.44 Mn OD2 A:Asp124 3.51 Mn OD1 A:Asp124 2.19 Mn C A:Asp124 5.00 Mn CG A:Asp124 3.14 Mn CA A:Asp124 4.84 Mn N A:Ala125 4.34 Mn CB A:Ala125 4.73 Mn HB3 A:Ala125 3.91 Mn H A:Ala125 3.82 Mn C A:Ala125 4.94 Mn CA A:Ala125 4.89 Mn HB2 A:His126 3.00 Mn N A:His126 4.15 Mn CB A:His126 3.61 Mn HB3 A:His126 4.32 Mn CD2 A:His126 4.40 Mn CG A:His126 3.29 Mn CA A:His126 4.54 Mn NE2 A:His126 4.33 Mn HE1 A:His126 3.31 Mn ND1 A:His126 2.23 Mn H A:His126 3.57 Mn CE1 A:His126 3.19 Mn OD2 A:Asp128 4.82 Mn OD1 A:Asp128 4.53 Mn HB2 A:Asp232 4.44 Mn CB A:Asp232 4.18 Mn HB3 A:Asp232 4.04 Mn OD2 A:Asp232 2.29 Mn OD1 A:Asp232 3.67 Mn CG A:Asp232 3.12 Mn HB2 A:Asp234 4.59 Mn CB A:Asp234 4.17 Mn HB3 A:Asp234 4.51 Mn OD2 A:Asp234 2.39 Mn H A:Asp234 4.85 Mn OD1 A:Asp234 2.16 Mn CG A:Asp234 2.69 Mn HB A:Thr246 4.42 Mn HG3 A:Glu277 4.64 Mn MN A:Mn2363 3.33 Mn HCD2 A:Abh551 4.77 Mn HCE1 A:Abh551 4.93 Mn O1 A:Abh551 2.13 Mn HO2 A:Abh551 4.58 Mn CD A:Abh551 4.41 Mn HCD1 A:Abh551 3.74 Mn O3 A:Abh551 2.80 Mn HO1 A:Abh551 2.72 Mn O2 A:Abh551 3.91 Mn HO3 A:Abh551 3.54 Mn CE A:Abh551 4.19 Mn B A:Abh551 3.05 Mn HCE2 A:Abh551 4.58 Mn O A:Hoh2391 4.87 Mn O A:Hoh2465 4.62 interactive model: Manganese binding site 2 out of 4 in 2aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2aeb. 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: Mn2362, A: Abh551, conact list: Atom Atom Distance (A) Mn HB2 A:His101 3.26 Mn CB A:His101 3.52 Mn HB3 A:His101 3.43 Mn CD2 A:His101 4.35 Mn CG A:His101 3.20 Mn NE2 A:His101 4.32 Mn HE1 A:His101 3.34 Mn ND1 A:His101 2.22 Mn CE1 A:His101 3.19 Mn CZ2 A:Trp122 4.65 Mn HE1 A:Trp122 3.69 Mn CE2 A:Trp122 4.85 Mn NE1 A:Trp122 4.39 Mn HZ2 A:Trp122 3.96 Mn HB2 A:Asp124 4.45 Mn CB A:Asp124 4.41 Mn HB3 A:Asp124 4.87 Mn OD2 A:Asp124 2.07 Mn OD1 A:Asp124 3.43 Mn CG A:Asp124 3.04 Mn HB2 A:His126 3.95 Mn CB A:His126 4.91 Mn HB2 A:Asp128 4.61 Mn CB A:Asp128 4.44 Mn HB3 A:Asp128 4.71 Mn OD2 A:Asp128 2.09 Mn OD1 A:Asp128 3.37 Mn CG A:Asp128 3.03 Mn O A:His141 4.45 Mn HB2 A:Asp232 3.05 Mn CB A:Asp232 3.59 Mn HB3 A:Asp232 3.81 Mn OD2 A:Asp232 2.24 Mn OD1 A:Asp232 4.39 Mn CG A:Asp232 3.25 Mn CA A:Asp232 4.95 Mn HG3 A:Glu277 4.11 Mn CG A:Glu277 4.95 Mn HG2 A:Glu277 4.94 Mn MN A:Mn2362 3.33 Mn HCE1 A:Abh551 4.61 Mn O1 A:Abh551 2.23 Mn HO2 A:Abh551 2.66 Mn O3 A:Abh551 3.55 Mn HO1 A:Abh551 2.37 Mn O2 A:Abh551 2.26 Mn HO3 A:Abh551 4.32 Mn CE A:Abh551 4.11 Mn B A:Abh551 2.82 Mn HCE2 A:Abh551 4.06 interactive model: Manganese binding site 3 out of 4 in 2aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2aeb. 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: Mn1363, B: Abh552, B: Hoh1383, B: Hoh1453, conact list: Atom Atom Distance (A) Mn CB B:Asp124 4.48 Mn HB3 B:Asp124 4.97 Mn HA B:Asp124 4.45 Mn OD2 B:Asp124 3.62 Mn OD1 B:Asp124 2.21 Mn C B:Asp124 4.99 Mn CG B:Asp124 3.19 Mn CA B:Asp124 4.82 Mn N B:Ala125 4.35 Mn CB B:Ala125 4.81 Mn HB3 B:Ala125 4.01 Mn H B:Ala125 3.83 Mn C B:Ala125 4.92 Mn CA B:Ala125 4.92 Mn HB2 B:His126 3.14 Mn N B:His126 4.18 Mn CB B:His126 3.71 Mn HB3 B:His126 4.44 Mn CD2 B:His126 4.41 Mn CG B:His126 3.32 Mn CA B:His126 4.59 Mn NE2 B:His126 4.32 Mn HE1 B:His126 3.31 Mn ND1 B:His126 2.28 Mn H B:His126 3.65 Mn CE1 B:His126 3.21 Mn OD2 B:Asp128 4.56 Mn OD1 B:Asp128 4.86 Mn HB2 B:Asp232 4.44 Mn CB B:Asp232 4.17 Mn HB3 B:Asp232 4.04 Mn OD2 B:Asp232 2.32 Mn OD1 B:Asp232 3.63 Mn CG B:Asp232 3.13 Mn HB2 B:Asp234 4.45 Mn CB B:Asp234 4.06 Mn HB3 B:Asp234 4.51 Mn OD2 B:Asp234 2.10 Mn H B:Asp234 4.83 Mn OD1 B:Asp234 2.39 Mn CG B:Asp234 2.55 Mn HB B:Thr246 4.37 Mn HG3 B:Glu277 4.58 Mn MN B:Mn1363 3.34 Mn HCD2 B:Abh552 4.44 Mn HCE1 B:Abh552 4.91 Mn O1 B:Abh552 2.21 Mn HO2 B:Abh552 4.64 Mn CD B:Abh552 4.32 Mn HCD1 B:Abh552 3.73 Mn O3 B:Abh552 2.74 Mn HO1 B:Abh552 2.86 Mn O2 B:Abh552 3.92 Mn HO3 B:Abh552 3.46 Mn CE B:Abh552 4.17 Mn B B:Abh552 3.08 Mn HCE2 B:Abh552 4.60 Mn O B:Hoh1383 4.56 Mn O B:Hoh1453 4.89 interactive model: Manganese binding site 4 out of 4 in 2aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2aeb. 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: Mn1362, B: Abh552, conact list: Atom Atom Distance (A) Mn HB2 B:His101 3.25 Mn CB B:His101 3.55 Mn HB3 B:His101 3.50 Mn CD2 B:His101 4.36 Mn CG B:His101 3.24 Mn NE2 B:His101 4.29 Mn HE1 B:His101 3.32 Mn ND1 B:His101 2.23 Mn CE1 B:His101 3.17 Mn CZ2 B:Trp122 4.63 Mn HE1 B:Trp122 3.60 Mn CE2 B:Trp122 4.85 Mn NE1 B:Trp122 4.32 Mn HZ2 B:Trp122 3.93 Mn HB2 B:Asp124 4.45 Mn CB B:Asp124 4.40 Mn HB3 B:Asp124 4.86 Mn OD2 B:Asp124 2.15 Mn OD1 B:Asp124 3.36 Mn CG B:Asp124 3.02 Mn HB2 B:His126 4.01 Mn CB B:His126 4.97 Mn HB2 B:Asp128 4.62 Mn CB B:Asp128 4.45 Mn HB3 B:Asp128 4.73 Mn OD2 B:Asp128 3.40 Mn OD1 B:Asp128 2.13 Mn CG B:Asp128 3.07 Mn O B:His141 4.56 Mn HB2 B:Asp232 3.01 Mn CB B:Asp232 3.54 Mn HB3 B:Asp232 3.81 Mn OD2 B:Asp232 2.23 Mn OD1 B:Asp232 4.37 Mn CG B:Asp232 3.22 Mn CA B:Asp232 4.91 Mn OD2 B:Asp234 4.97 Mn OD1 B:Asp234 4.86 Mn HG3 B:Glu277 4.08 Mn OE2 B:Glu277 4.98 Mn CG B:Glu277 4.90 Mn HG2 B:Glu277 4.87 Mn MN B:Mn1362 3.34 Mn HCE1 B:Abh552 4.63 Mn O1 B:Abh552 2.13 Mn HO2 B:Abh552 2.64 Mn HCD1 B:Abh552 4.97 Mn O3 B:Abh552 3.58 Mn HO1 B:Abh552 2.25 Mn O2 B:Abh552 2.27 Mn HO3 B:Abh552 4.30 Mn CE B:Abh552 4.08 Mn B B:Abh552 2.81 Mn HCE2 B:Abh552 4.01 interactive model: