Manganese in the structure of Crystal Structure Of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily (pdb 1woi)

The binding sites of Manganese atom in the structure of Crystal Structure Of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily (pdb code 1woi). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1woi structure was solved by H.J.AHN, K.H.KIM, J.LEE, J.-Y.HA, H.H.LEE, D.KIM, H.-J.YOON, A.-R.KWON, S.W.SUH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.9 Space group P212121 a (A) 81.764 b (A) 130.759 c (A) 168.746 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21 Rfree (%) 24.1 Manganese Binding Sites: Manganese binding site 1 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1woi. 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: His121, A: Gln141, A: Asp143, A: His145, A: Asp147, A: Asn159, A: Asp229, A: Asp231, A: Glu274, A: Mn1502, A: Hoh1636, conact list: Atom Atom Distance (A) Mn NE2 A:His121 4.03 Mn CB A:His121 3.58 Mn ND1 A:His121 2.02 Mn CD2 A:His121 4.17 Mn CE1 A:His121 2.87 Mn CG A:His121 3.12 Mn NE2 A:Gln141 4.77 Mn CB A:Asp143 4.33 Mn OD2 A:Asp143 2.12 Mn OD1 A:Asp143 3.07 Mn CG A:Asp143 2.92 Mn O A:His145 4.72 Mn CB A:His145 4.81 Mn ND1 A:His145 4.73 Mn CB A:Asp147 4.43 Mn OD2 A:Asp147 2.07 Mn OD1 A:Asp147 3.77 Mn CG A:Asp147 3.23 Mn O A:Asn159 4.92 Mn CB A:Asp229 3.70 Mn OD2 A:Asp229 2.18 Mn OD1 A:Asp229 4.35 Mn CG A:Asp229 3.26 Mn OD2 A:Asp231 4.80 Mn OD1 A:Asp231 4.91 Mn CG A:Glu274 4.73 Mn MN A:Mn1502 3.01 Mn O A:Hoh1636 2.38 interactive model: Manganese binding site 2 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1woi. 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: His121, A: Asp143, A: Ala144, A: His145, A: Asp147, A: Asp229, A: Asp231, A: Glu274, A: Mn1501, A: Hoh1520, A: Hoh1636, conact list: Atom Atom Distance (A) Mn ND1 A:His121 4.86 Mn CB A:Asp143 4.58 Mn OD2 A:Asp143 3.65 Mn C A:Asp143 4.94 Mn OD1 A:Asp143 2.25 Mn CG A:Asp143 3.27 Mn CA A:Asp143 4.82 Mn N A:Ala144 4.11 Mn C A:Ala144 4.75 Mn CB A:Ala144 4.72 Mn CA A:Ala144 4.80 Mn NE2 A:His145 4.33 Mn N A:His145 3.91 Mn CB A:His145 3.79 Mn ND1 A:His145 2.31 Mn CD2 A:His145 4.48 Mn CE1 A:His145 3.15 Mn CG A:His145 3.40 Mn CA A:His145 4.45 Mn OD2 A:Asp147 4.35 Mn OD1 A:Asp147 4.95 Mn CB A:Asp229 4.14 Mn OD2 A:Asp229 2.33 Mn OD1 A:Asp229 3.52 Mn CG A:Asp229 3.09 Mn CB A:Asp231 4.15 Mn OD2 A:Asp231 2.22 Mn OD1 A:Asp231 2.44 Mn CG A:Asp231 2.65 Mn CG A:Glu274 5.00 Mn MN A:Mn1501 3.01 Mn O A:Hoh1520 4.70 Mn O A:Hoh1636 2.56 interactive model: Manganese binding site 3 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1woi. 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: His121, B: Gln141, B: Asp143, B: His145, B: Asp147, B: Asn159, B: Asp229, B: Asp231, B: Glu274, B: Mn1504, B: Hoh1581, B: Hoh1601, conact list: Atom Atom Distance (A) Mn NE2 B:His121 4.13 Mn CB B:His121 3.57 Mn ND1 B:His121 2.12 Mn CD2 B:His121 4.23 Mn CE1 B:His121 2.99 Mn CG B:His121 3.16 Mn NE2 B:Gln141 4.84 Mn CB B:Asp143 4.49 Mn OD2 B:Asp143 2.32 Mn OD1 B:Asp143 3.16 Mn CG B:Asp143 3.07 Mn O B:His145 4.85 Mn CB B:His145 4.85 Mn ND1 B:His145 4.92 Mn CB B:Asp147 4.42 Mn OD2 B:Asp147 2.08 Mn OD1 B:Asp147 3.77 Mn CG B:Asp147 3.22 Mn O B:Asn159 4.67 Mn CB B:Asp229 3.73 Mn OD2 B:Asp229 2.13 Mn OD1 B:Asp229 4.32 Mn CG B:Asp229 3.24 Mn OD2 B:Asp231 4.80 Mn OD1 B:Asp231 4.99 Mn CG B:Glu274 4.65 Mn MN B:Mn1504 2.92 Mn O B:Hoh1581 4.93 Mn O B:Hoh1601 2.61 interactive model: Manganese binding site 4 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1woi. 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: His121, B: Asp143, B: Ala144, B: His145, B: Asp147, B: Asp229, B: Asp231, B: Glu274, B: Mn1503, B: Hoh1521, B: Hoh1601, conact list: Atom Atom Distance (A) Mn ND1 B:His121 4.83 Mn CB B:Asp143 4.67 Mn OD2 B:Asp143 3.71 Mn OD1 B:Asp143 2.36 Mn CG B:Asp143 3.36 Mn CA B:Asp143 4.90 Mn N B:Ala144 4.21 Mn C B:Ala144 4.89 Mn CB B:Ala144 4.83 Mn CA B:Ala144 4.92 Mn NE2 B:His145 4.62 Mn N B:His145 4.03 Mn CB B:His145 3.89 Mn ND1 B:His145 2.59 Mn CD2 B:His145 4.72 Mn CE1 B:His145 3.46 Mn CG B:His145 3.61 Mn CA B:His145 4.56 Mn OD2 B:Asp147 4.25 Mn CB B:Asp229 4.07 Mn OD2 B:Asp229 2.37 Mn OD1 B:Asp229 3.50 Mn CG B:Asp229 3.06 Mn CB B:Asp231 4.24 Mn OD2 B:Asp231 2.26 Mn OD1 B:Asp231 2.53 Mn CG B:Asp231 2.73 Mn CG B:Glu274 4.90 Mn MN B:Mn1503 2.92 Mn O B:Hoh1521 4.76 Mn O B:Hoh1601 2.90 interactive model: Manganese binding site 5 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 1woi. 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: His121, C: Gln141, C: Asp143, C: His145, C: Asp147, C: Asp229, C: Asp231, C: Glu274, C: Mn1506, C: Hoh1611, C: Hoh1630, conact list: Atom Atom Distance (A) Mn NE2 C:His121 4.04 Mn CB C:His121 3.61 Mn ND1 C:His121 2.03 Mn CD2 C:His121 4.19 Mn CE1 C:His121 2.87 Mn CG C:His121 3.14 Mn NE2 C:Gln141 4.72 Mn CB C:Asp143 4.41 Mn OD2 C:Asp143 2.23 Mn OD1 C:Asp143 3.11 Mn CG C:Asp143 3.00 Mn O C:His145 4.71 Mn ND1 C:His145 4.85 Mn CB C:Asp147 4.50 Mn OD2 C:Asp147 2.14 Mn OD1 C:Asp147 3.83 Mn CG C:Asp147 3.30 Mn CB C:Asp229 3.65 Mn OD2 C:Asp229 2.14 Mn OD1 C:Asp229 4.31 Mn CG C:Asp229 3.21 Mn OD2 C:Asp231 4.85 Mn OD1 C:Asp231 4.91 Mn CG C:Glu274 4.65 Mn MN C:Mn1506 2.89 Mn O C:Hoh1611 4.91 Mn O C:Hoh1630 2.64 interactive model: Manganese binding site 6 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 1woi. 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: His121, C: Asp143, C: Ala144, C: His145, C: Asp147, C: Asp229, C: Asp231, C: Glu274, C: Mn1505, C: Hoh1517, C: Hoh1630, conact list: Atom Atom Distance (A) Mn ND1 C:His121 4.79 Mn CB C:Asp143 4.52 Mn OD2 C:Asp143 3.60 Mn C C:Asp143 4.91 Mn OD1 C:Asp143 2.26 Mn CG C:Asp143 3.23 Mn CA C:Asp143 4.74 Mn N C:Ala144 4.14 Mn C C:Ala144 4.85 Mn CB C:Ala144 4.84 Mn CA C:Ala144 4.89 Mn O C:His145 4.81 Mn NE2 C:His145 4.46 Mn N C:His145 3.92 Mn CB C:His145 3.90 Mn ND1 C:His145 2.46 Mn CD2 C:His145 4.61 Mn CE1 C:His145 3.28 Mn CG C:His145 3.54 Mn CA C:His145 4.48 Mn OD2 C:Asp147 4.22 Mn OD1 C:Asp147 4.89 Mn CG C:Asp147 4.98 Mn CB C:Asp229 4.01 Mn OD2 C:Asp229 2.24 Mn OD1 C:Asp229 3.50 Mn CG C:Asp229 3.00 Mn CB C:Asp231 4.26 Mn OD2 C:Asp231 2.32 Mn OD1 C:Asp231 2.51 Mn CG C:Asp231 2.75 Mn CG C:Glu274 4.97 Mn MN C:Mn1505 2.89 Mn O C:Hoh1517 4.78 Mn O C:Hoh1630 2.73 interactive model: Manganese binding site 7 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 1woi. 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: D: His121, D: Gln141, D: Asp143, D: His145, D: Asp147, D: Asn159, D: Asp229, D: Asp231, D: Glu274, D: Mn1508, D: Hoh1600, conact list: Atom Atom Distance (A) Mn NE2 D:His121 4.01 Mn CB D:His121 3.57 Mn ND1 D:His121 2.03 Mn CD2 D:His121 4.15 Mn CE1 D:His121 2.87 Mn CG D:His121 3.11 Mn NE2 D:Gln141 4.69 Mn CB D:Asp143 4.39 Mn OD2 D:Asp143 2.19 Mn OD1 D:Asp143 3.10 Mn CG D:Asp143 2.98 Mn O D:His145 4.85 Mn ND1 D:His145 4.92 Mn CB D:Asp147 4.41 Mn OD2 D:Asp147 2.10 Mn OD1 D:Asp147 3.81 Mn CG D:Asp147 3.24 Mn O D:Asn159 4.66 Mn CB D:Asp229 3.69 Mn OD2 D:Asp229 2.20 Mn OD1 D:Asp229 4.36 Mn CG D:Asp229 3.26 Mn OD2 D:Asp231 4.92 Mn OD1 D:Asp231 4.94 Mn CG D:Glu274 4.73 Mn MN D:Mn1508 3.07 Mn O D:Hoh1600 2.78 interactive model: Manganese binding site 8 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 1woi. 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: D: His121, D: Asp143, D: Ala144, D: His145, D: Asp147, D: Asp229, D: Asp231, D: Mn1507, D: Hoh1524, D: Hoh1600, conact list: Atom Atom Distance (A) Mn ND1 D:His121 4.91 Mn CB D:Asp143 4.58 Mn OD2 D:Asp143 3.70 Mn C D:Asp143 4.94 Mn OD1 D:Asp143 2.28 Mn CG D:Asp143 3.30 Mn CA D:Asp143 4.80 Mn N D:Ala144 4.12 Mn C D:Ala144 4.83 Mn CB D:Ala144 4.74 Mn CA D:Ala144 4.84 Mn NE2 D:His145 4.40 Mn N D:His145 3.98 Mn CB D:His145 3.91 Mn ND1 D:His145 2.42 Mn CD2 D:His145 4.56 Mn CE1 D:His145 3.21 Mn CG D:His145 3.51 Mn CA D:His145 4.54 Mn OD2 D:Asp147 4.25 Mn OD1 D:Asp147 4.90 Mn CB D:Asp229 4.11 Mn OD2 D:Asp229 2.25 Mn OD1 D:Asp229 3.55 Mn CG D:Asp229 3.06 Mn CB D:Asp231 4.17 Mn OD2 D:Asp231 2.22 Mn OD1 D:Asp231 2.47 Mn CG D:Asp231 2.67 Mn MN D:Mn1507 3.07 Mn O D:Hoh1524 4.73 Mn O D:Hoh1600 3.05 interactive model: Manganese binding site 9 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Manganese in the PDB 1woi. 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: E: His121, E: Gln141, E: Asp143, E: His145, E: Asp147, E: Asn159, E: Asp229, E: Asp231, E: Glu274, E: Mn1510, E: Hoh1616, conact list: Atom Atom Distance (A) Mn NE2 E:His121 4.19 Mn CB E:His121 3.47 Mn ND1 E:His121 2.14 Mn CD2 E:His121 4.23 Mn CE1 E:His121 3.08 Mn CG E:His121 3.13 Mn CA E:His121 4.97 Mn NE2 E:Gln141 4.87 Mn CB E:Asp143 4.61 Mn OD2 E:Asp143 2.43 Mn OD1 E:Asp143 3.26 Mn CG E:Asp143 3.19 Mn O E:His145 4.88 Mn ND1 E:His145 4.96 Mn CB E:Asp147 4.33 Mn OD2 E:Asp147 2.07 Mn OD1 E:Asp147 3.71 Mn CG E:Asp147 3.16 Mn O E:Asn159 4.63 Mn CB E:Asp229 3.90 Mn OD2 E:Asp229 2.22 Mn OD1 E:Asp229 4.42 Mn CG E:Asp229 3.36 Mn OD2 E:Asp231 4.82 Mn CG E:Glu274 4.65 Mn MN E:Mn1510 2.99 Mn O E:Hoh1616 2.35 interactive model: Manganese binding site 10 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Manganese in the PDB 1woi. 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: E: His121, E: Asp143, E: Ala144, E: His145, E: Asp147, E: Asp229, E: Asp231, E: Glu274, E: Mn1509, E: Hoh1582, E: Hoh1616, conact list: Atom Atom Distance (A) Mn ND1 E:His121 4.93 Mn CB E:Asp143 4.74 Mn OD2 E:Asp143 3.75 Mn OD1 E:Asp143 2.38 Mn CG E:Asp143 3.40 Mn N E:Ala144 4.27 Mn C E:Ala144 4.91 Mn CB E:Ala144 4.80 Mn CA E:Ala144 4.94 Mn NE2 E:His145 4.40 Mn N E:His145 4.05 Mn CB E:His145 3.91 Mn ND1 E:His145 2.48 Mn CD2 E:His145 4.54 Mn CE1 E:His145 3.25 Mn CG E:His145 3.51 Mn CA E:His145 4.58 Mn OD2 E:Asp147 4.06 Mn OD1 E:Asp147 4.85 Mn CG E:Asp147 4.88 Mn CB E:Asp229 4.26 Mn OD2 E:Asp229 2.46 Mn OD1 E:Asp229 3.65 Mn CG E:Asp229 3.22 Mn CB E:Asp231 4.31 Mn OD2 E:Asp231 2.31 Mn OD1 E:Asp231 2.61 Mn CG E:Asp231 2.80 Mn CG E:Glu274 4.99 Mn MN E:Mn1509 2.99 Mn O E:Hoh1582 4.72 Mn O E:Hoh1616 2.52 interactive model: Manganese binding site 11 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Manganese in the PDB 1woi. 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: F: His121, F: Gln141, F: Asp143, F: His145, F: Asp147, F: Asn159, F: Asp229, F: Asp231, F: Glu274, F: Mn1512, F: Hoh1618, F: Hoh1627, conact list: Atom Atom Distance (A) Mn NE2 F:His121 4.06 Mn CB F:His121 3.51 Mn ND1 F:His121 2.03 Mn CD2 F:His121 4.15 Mn CE1 F:His121 2.92 Mn CG F:His121 3.08 Mn CA F:His121 4.98 Mn NE2 F:Gln141 4.72 Mn CB F:Asp143 4.45 Mn OD2 F:Asp143 2.25 Mn OD1 F:Asp143 3.22 Mn CG F:Asp143 3.06 Mn O F:His145 4.76 Mn CB F:His145 4.97 Mn CB F:Asp147 4.49 Mn OD2 F:Asp147 2.17 Mn OD1 F:Asp147 3.90 Mn CG F:Asp147 3.33 Mn O F:Asn159 4.72 Mn CB F:Asp229 3.65 Mn OD2 F:Asp229 2.17 Mn OD1 F:Asp229 4.34 Mn CG F:Asp229 3.23 Mn OD2 F:Asp231 4.88 Mn OD1 F:Asp231 4.99 Mn CG F:Glu274 4.65 Mn MN F:Mn1512 3.03 Mn O F:Hoh1618 4.69 Mn O F:Hoh1627 2.59 interactive model: Manganese binding site 12 out of 12 in 1woi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Manganese in the PDB 1woi. 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: F: His121, F: Asp143, F: Ala144, F: His145, F: Asp147, F: Asp229, F: Asp231, F: Glu274, F: Mn1511, F: Hoh1531, F: Hoh1627, conact list: Atom Atom Distance (A) Mn ND1 F:His121 4.89 Mn CB F:Asp143 4.61 Mn OD2 F:Asp143 3.64 Mn C F:Asp143 4.98 Mn OD1 F:Asp143 2.30 Mn CG F:Asp143 3.29 Mn CA F:Asp143 4.84 Mn N F:Ala144 4.17 Mn C F:Ala144 4.86 Mn CB F:Ala144 4.81 Mn CA F:Ala144 4.89 Mn O F:His145 4.98 Mn NE2 F:His145 4.60 Mn N F:His145 4.00 Mn CB F:His145 3.90 Mn ND1 F:His145 2.58 Mn CD2 F:His145 4.70 Mn CE1 F:His145 3.44 Mn CG F:His145 3.60 Mn CA F:His145 4.55 Mn OD2 F:Asp147 4.28 Mn CB F:Asp229 4.04 Mn OD2 F:Asp229 2.22 Mn OD1 F:Asp229 3.46 Mn CG F:Asp229 2.99 Mn CB F:Asp231 4.18 Mn OD2 F:Asp231 2.19 Mn OD1 F:Asp231 2.49 Mn CG F:Asp231 2.66 Mn CG F:Glu274 4.85 Mn MN F:Mn1511 3.03 Mn O F:Hoh1531 4.69 Mn O F:Hoh1627 2.76 interactive model: