Manganese in the structure of Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed With Amp and Mn Ion From Francisella Tularensis (pdb 2qjt)

The binding sites of Manganese atom in the structure of Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed With Amp and Mn Ion From Francisella Tularensis (pdb code 2qjt). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2qjt structure was solved by N.HUANG, L.SORCI, X.ZHANG, C.BRAUTIGAN, N.RAFFAELLI, G.MAGNI, N.V.GRISHIN, A.OSTERMAN, H.ZHANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 33.6-2.3 Space group F222 a (A) 125.644 b (A) 163.645 c (A) 179.967 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.4 Rfree (%) 24.9 Manganese Binding Sites: Manganese binding site 1 out of 9 in 2qjt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2qjt. 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: Gly235, B: Phe236, B: Glu238, B: Arg249, B: Glu250, B: Glu253, B: Asp307, B: Mn506, B: Amp602, B: Hoh675, B: Hoh676, B: Hoh677, B: Hoh678, B: Hoh679, B: Hoh680, B: Hoh686, B: Hoh687, conact list: Atom Atom Distance (A) Mn C B:Gly235 4.72 Mn CA B:Gly235 4.73 Mn O B:Phe236 4.18 Mn N B:Phe236 4.01 Mn CB B:Phe236 4.73 Mn C B:Phe236 4.91 Mn CA B:Phe236 4.75 Mn OE1 B:Glu238 3.97 Mn CZ B:Arg249 4.86 Mn NH2 B:Arg249 4.00 Mn NH1 B:Arg249 4.80 Mn OE1 B:Glu250 3.69 Mn OE2 B:Glu250 2.22 Mn CD B:Glu250 3.29 Mn CG B:Glu250 4.57 Mn OE2 B:Glu253 4.33 Mn OD2 B:Asp307 4.70 Mn MN B:Mn506 3.88 Mn P B:Amp602 3.46 Mn O3P B:Amp602 2.24 Mn O4' B:Amp602 4.30 Mn O1P B:Amp602 4.75 Mn C4' B:Amp602 4.91 Mn O5' B:Amp602 3.96 Mn O2P B:Amp602 3.98 Mn O B:Hoh675 2.30 Mn O B:Hoh676 2.13 Mn O B:Hoh677 2.16 Mn O B:Hoh678 4.11 Mn O B:Hoh679 4.11 Mn O B:Hoh680 4.27 Mn O B:Hoh686 4.81 Mn O B:Hoh687 2.19 interactive model: Manganese binding site 2 out of 9 in 2qjt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2qjt. 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: Gly234, B: Gly235, B: Glu250, B: Glu253, B: Glu254, B: Asp307, B: Asp308, B: Mn505, B: Mn507, B: Amp602, B: Hoh675, B: Hoh680, B: Hoh685, B: Hoh686, B: Hoh687, conact list: Atom Atom Distance (A) Mn O B:Gly234 3.85 Mn C B:Gly234 4.68 Mn CA B:Gly235 4.75 Mn OE1 B:Glu250 2.17 Mn CB B:Glu250 4.89 Mn OE2 B:Glu250 3.60 Mn CD B:Glu250 3.23 Mn CG B:Glu250 4.58 Mn OE2 B:Glu253 3.92 Mn OE1 B:Glu254 2.01 Mn OE2 B:Glu254 4.19 Mn CD B:Glu254 3.10 Mn CG B:Glu254 3.52 Mn CB B:Asp307 4.36 Mn OD2 B:Asp307 3.44 Mn CG B:Asp307 4.18 Mn N B:Asp308 4.73 Mn CB B:Asp308 4.84 Mn OD2 B:Asp308 2.48 Mn OD1 B:Asp308 3.68 Mn CG B:Asp308 3.44 Mn MN B:Mn505 3.88 Mn MN B:Mn507 3.23 Mn P B:Amp602 3.48 Mn O3P B:Amp602 3.84 Mn O1P B:Amp602 4.78 Mn O5' B:Amp602 3.85 Mn O2P B:Amp602 2.42 Mn O B:Hoh675 4.63 Mn O B:Hoh680 3.77 Mn O B:Hoh685 5.00 Mn O B:Hoh686 2.48 Mn O B:Hoh687 1.93 interactive model: Manganese binding site 3 out of 9 in 2qjt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2qjt. 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: Arg221, B: Gly234, B: Gly235, B: Glu250, B: Glu254, B: Asp308, B: Mn506, B: Amp602, B: Hoh681, B: Hoh682, B: Hoh684, B: Hoh685, B: Hoh687, B: Hoh743, conact list: Atom Atom Distance (A) Mn NH1 B:Arg221 4.14 Mn O B:Gly234 2.14 Mn N B:Gly234 4.37 Mn C B:Gly234 3.35 Mn CA B:Gly234 4.44 Mn N B:Gly235 4.11 Mn CA B:Gly235 3.97 Mn OE1 B:Glu250 4.18 Mn OE1 B:Glu254 2.40 Mn OE2 B:Glu254 3.34 Mn CD B:Glu254 3.22 Mn CG B:Glu254 4.63 Mn CB B:Asp308 4.54 Mn OD2 B:Asp308 3.47 Mn OD1 B:Asp308 2.21 Mn CG B:Asp308 3.17 Mn MN B:Mn506 3.23 Mn P B:Amp602 3.42 Mn O3P B:Amp602 4.55 Mn O1P B:Amp602 3.67 Mn O5' B:Amp602 4.20 Mn O2P B:Amp602 2.07 Mn O B:Hoh681 4.13 Mn O B:Hoh682 4.32 Mn O B:Hoh684 2.30 Mn O B:Hoh685 2.22 Mn O B:Hoh687 4.66 Mn O B:Hoh743 4.88 interactive model: Manganese binding site 4 out of 9 in 2qjt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2qjt. 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: His215, B: Leu300, B: Ser316, B: Hoh795, B: Hoh796, conact list: Atom Atom Distance (A) Mn NE2 B:His215 2.50 Mn ND1 B:His215 4.52 Mn CD2 B:His215 3.44 Mn CE1 B:His215 3.41 Mn CG B:His215 4.57 Mn CD1 B:Leu300 4.78 Mn CB B:Ser316 4.62 Mn O B:Hoh795 2.61 Mn O B:Hoh796 2.83 interactive model: Manganese binding site 5 out of 9 in 2qjt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 2qjt. 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: Arg221, A: Gly234, A: Gly235, A: Glu250, A: Glu254, A: Asp308, A: Mn503, A: Amp601, A: Hoh693, A: Hoh694, A: Hoh695, A: Hoh696, A: Hoh700, A: Hoh720, conact list: Atom Atom Distance (A) Mn NH1 A:Arg221 4.21 Mn O A:Gly234 2.15 Mn N A:Gly234 4.34 Mn C A:Gly234 3.35 Mn CA A:Gly234 4.44 Mn N A:Gly235 4.09 Mn CA A:Gly235 3.96 Mn OE1 A:Glu250 4.27 Mn OE1 A:Glu254 3.39 Mn OE2 A:Glu254 2.15 Mn CD A:Glu254 3.11 Mn CG A:Glu254 4.44 Mn CB A:Asp308 4.58 Mn OD2 A:Asp308 3.42 Mn OD1 A:Asp308 2.26 Mn CG A:Asp308 3.18 Mn MN A:Mn503 3.31 Mn P A:Amp601 3.31 Mn O3P A:Amp601 4.47 Mn O1P A:Amp601 3.63 Mn O5' A:Amp601 3.99 Mn O2P A:Amp601 2.02 Mn O A:Hoh693 2.18 Mn O A:Hoh694 2.21 Mn O A:Hoh695 4.03 Mn O A:Hoh696 4.19 Mn O A:Hoh700 4.88 Mn O A:Hoh720 4.42 interactive model: Manganese binding site 6 out of 9 in 2qjt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 2qjt. 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: Gln175, A: Gln178, A: Hoh679, conact list: Atom Atom Distance (A) Mn NE2 A:Gln175 3.60 Mn OE1 A:Gln175 2.38 Mn CB A:Gln175 4.94 Mn CD A:Gln175 3.30 Mn CG A:Gln175 4.65 Mn CA A:Gln175 4.89 Mn NE2 A:Gln178 2.85 Mn OE1 A:Gln178 2.47 Mn CB A:Gln178 4.85 Mn CD A:Gln178 2.96 Mn CG A:Gln178 4.40 Mn O A:Hoh679 2.56 interactive model: Manganese binding site 7 out of 9 in 2qjt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 2qjt. 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: Gly234, A: Gly235, A: Glu250, A: Glu253, A: Glu254, A: Asp307, A: Asp308, A: Mn501, A: Mn504, A: Amp601, A: Hoh694, A: Hoh704, A: Hoh710, A: Hoh711, A: Hoh790, A: Hoh794, conact list: Atom Atom Distance (A) Mn O A:Gly234 4.09 Mn C A:Gly234 4.81 Mn CA A:Gly235 4.82 Mn OE1 A:Glu250 2.28 Mn CB A:Glu250 4.94 Mn OE2 A:Glu250 3.67 Mn CD A:Glu250 3.33 Mn CG A:Glu250 4.65 Mn OE2 A:Glu253 4.00 Mn OE1 A:Glu254 4.33 Mn CB A:Glu254 4.93 Mn OE2 A:Glu254 2.22 Mn CD A:Glu254 3.17 Mn CG A:Glu254 3.41 Mn CB A:Asp307 4.76 Mn OD2 A:Asp307 4.15 Mn CG A:Asp307 4.58 Mn N A:Asp308 4.86 Mn CB A:Asp308 4.78 Mn OD2 A:Asp308 2.39 Mn OD1 A:Asp308 3.72 Mn CG A:Asp308 3.41 Mn MN A:Mn501 3.31 Mn MN A:Mn504 3.90 Mn P A:Amp601 3.45 Mn O3P A:Amp601 3.79 Mn O1P A:Amp601 4.78 Mn O5' A:Amp601 3.68 Mn O2P A:Amp601 2.37 Mn O A:Hoh694 4.98 Mn O A:Hoh704 4.79 Mn O A:Hoh710 2.26 Mn O A:Hoh711 2.60 Mn O A:Hoh790 4.02 Mn O A:Hoh794 4.72 interactive model: Manganese binding site 8 out of 9 in 2qjt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 2qjt. 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: Gly235, A: Phe236, A: Glu238, A: Arg249, A: Glu250, A: Glu253, A: Mn503, A: Amp601, A: Hoh701, A: Hoh702, A: Hoh703, A: Hoh704, A: Hoh705, A: Hoh710, A: Hoh711, A: Hoh712, A: Hoh790, A: Hoh794, conact list: Atom Atom Distance (A) Mn C A:Gly235 4.71 Mn CA A:Gly235 4.67 Mn O A:Phe236 4.26 Mn N A:Phe236 3.99 Mn CB A:Phe236 4.78 Mn C A:Phe236 4.99 Mn CA A:Phe236 4.79 Mn OE1 A:Glu238 4.44 Mn CZ A:Arg249 4.79 Mn NH2 A:Arg249 4.04 Mn NH1 A:Arg249 4.64 Mn OE1 A:Glu250 3.76 Mn OE2 A:Glu250 2.37 Mn CD A:Glu250 3.41 Mn CG A:Glu250 4.70 Mn OE2 A:Glu253 4.32 Mn MN A:Mn503 3.90 Mn P A:Amp601 3.47 Mn O3P A:Amp601 2.24 Mn O4' A:Amp601 4.23 Mn C5' A:Amp601 4.91 Mn O1P A:Amp601 4.67 Mn C4' A:Amp601 4.72 Mn O5' A:Amp601 3.99 Mn O2P A:Amp601 3.96 Mn O A:Hoh701 4.50 Mn O A:Hoh702 2.49 Mn O A:Hoh703 2.18 Mn O A:Hoh704 2.22 Mn O A:Hoh705 4.35 Mn O A:Hoh710 4.63 Mn O A:Hoh711 1.71 Mn O A:Hoh712 4.63 Mn O A:Hoh790 4.55 Mn O A:Hoh794 4.28 interactive model: Manganese binding site 9 out of 9 in 2qjt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Manganese in the PDB 2qjt. 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: His215, A: Leu300, A: Ser316, A: Hoh717, A: Hoh768, A: Hoh783, conact list: Atom Atom Distance (A) Mn NE2 A:His215 2.42 Mn ND1 A:His215 4.50 Mn CD2 A:His215 3.32 Mn CE1 A:His215 3.41 Mn CG A:His215 4.49 Mn CD1 A:Leu300 4.72 Mn CB A:Ser316 4.63 Mn OG A:Ser316 4.79 Mn O A:Hoh717 4.24 Mn O A:Hoh768 3.22 Mn O A:Hoh783 2.14 interactive model: