Manganese in the structure of Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed With Udp-Glcua and Udp (pdb 2z86)

The binding sites of Manganese atom in the structure of Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed With Udp-Glcua and Udp (pdb code 2z86). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2z86 structure was solved by T.OSAWA, N.SUGIURA, H.SHIMADA, R.HIROOKA, A.TSUJI, M.KIMURA, K.KIMATA, Y.KAKUTA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.4 Space group P1211 a (A) 84.092 b (A) 219.829 c (A) 85.856 alpha (°) 90.00 beta (°) 103.07 gamma (°) 90.00 Rfactor (%) 22.5 Rfree (%) 28.6 Manganese Binding Sites: Manganese binding site 1 out of 8 in 2z86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2z86. 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: Arg161, A: Asp239, A: Asp241, A: His386, A: Uga683, A: Hoh790, conact list: Atom Atom Distance (A) Mn CZ A:Arg161 4.19 Mn NH2 A:Arg161 3.14 Mn NH1 A:Arg161 4.36 Mn OD2 A:Asp239 4.52 Mn CB A:Asp241 4.40 Mn OD2 A:Asp241 2.51 Mn OD1 A:Asp241 3.31 Mn CG A:Asp241 3.15 Mn NE2 A:His386 2.24 Mn ND1 A:His386 4.05 Mn CD2 A:His386 3.35 Mn CE1 A:His386 2.89 Mn CG A:His386 4.30 Mn O3B A:Uga683 4.28 Mn C5D A:Uga683 4.83 Mn PA A:Uga683 3.39 Mn O2B A:Uga683 4.65 Mn O3A A:Uga683 3.74 Mn O5D A:Uga683 4.62 Mn O2A A:Uga683 4.25 Mn O1B A:Uga683 2.18 Mn C1' A:Uga683 4.79 Mn PB A:Uga683 3.44 Mn O1A A:Uga683 2.18 Mn O A:Hoh790 2.96 interactive model: Manganese binding site 2 out of 8 in 2z86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2z86. 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: Asp521, A: Asp522, A: Val629, A: His631, A: Uga684, conact list: Atom Atom Distance (A) Mn CB A:Asp521 4.34 Mn OD2 A:Asp521 2.51 Mn OD1 A:Asp521 2.73 Mn CG A:Asp521 2.92 Mn OD2 A:Asp522 4.55 Mn OD1 A:Asp522 4.09 Mn CG A:Asp522 4.70 Mn O A:Val629 4.12 Mn NE2 A:His631 4.65 Mn CE1 A:His631 4.01 Mn O3B A:Uga684 4.83 Mn C5D A:Uga684 4.96 Mn PA A:Uga684 3.56 Mn O3A A:Uga684 4.19 Mn O5D A:Uga684 4.74 Mn O2A A:Uga684 4.33 Mn O1B A:Uga684 2.59 Mn PB A:Uga684 3.95 Mn O1A A:Uga684 2.13 interactive model: Manganese binding site 3 out of 8 in 2z86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2z86. 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: Arg161, B: Asp239, B: Asp241, B: His386, B: Udp1, B: Hoh798, B: Hoh820, conact list: Atom Atom Distance (A) Mn NH2 B:Arg161 3.74 Mn OD2 B:Asp239 4.95 Mn CB B:Asp241 4.25 Mn OD2 B:Asp241 2.25 Mn OD1 B:Asp241 3.03 Mn CG B:Asp241 2.91 Mn NE2 B:His386 2.17 Mn ND1 B:His386 4.10 Mn CD2 B:His386 3.20 Mn CE1 B:His386 2.98 Mn CG B:His386 4.24 Mn O3B B:Udp1 4.37 Mn PA B:Udp1 3.32 Mn O2A B:Udp1 2.04 Mn O1B B:Udp1 2.18 Mn PB B:Udp1 3.46 Mn C5' B:Udp1 4.76 Mn O5' B:Udp1 4.47 Mn O2B B:Udp1 4.50 Mn O3A B:Udp1 3.61 Mn O1A B:Udp1 4.24 Mn O B:Hoh798 4.82 Mn O B:Hoh820 2.07 interactive model: Manganese binding site 4 out of 8 in 2z86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2z86. 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: Asp521, B: Asp522, B: Arg628, B: Val629, B: His631, B: Uga683, B: Hoh821, B: Hoh822, conact list: Atom Atom Distance (A) Mn CB B:Asp521 4.35 Mn OD2 B:Asp521 2.33 Mn OD1 B:Asp521 2.93 Mn CG B:Asp521 2.93 Mn OD2 B:Asp522 4.69 Mn OD1 B:Asp522 4.42 Mn CG B:Asp522 4.94 Mn NE B:Arg628 4.64 Mn O B:Val629 4.11 Mn NE2 B:His631 2.86 Mn ND1 B:His631 4.84 Mn CD2 B:His631 3.52 Mn CE1 B:His631 3.88 Mn CG B:His631 4.70 Mn O3B B:Uga683 4.25 Mn C5D B:Uga683 4.70 Mn PA B:Uga683 3.47 Mn C3D B:Uga683 4.93 Mn O2B B:Uga683 4.74 Mn O3A B:Uga683 3.89 Mn O5D B:Uga683 4.52 Mn O2A B:Uga683 4.52 Mn O1B B:Uga683 2.20 Mn PB B:Uga683 3.51 Mn O2' B:Uga683 4.99 Mn O1A B:Uga683 2.11 Mn O B:Hoh821 2.23 Mn O B:Hoh822 2.08 interactive model: Manganese binding site 5 out of 8 in 2z86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 2z86. 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: Arg161, C: Asp241, C: His386, C: Udp1, C: Hoh819, C: Hoh853, conact list: Atom Atom Distance (A) Mn CZ C:Arg161 4.85 Mn NH2 C:Arg161 4.74 Mn NH1 C:Arg161 4.19 Mn CB C:Asp241 4.58 Mn OD2 C:Asp241 2.34 Mn OD1 C:Asp241 3.59 Mn CG C:Asp241 3.28 Mn NE2 C:His386 2.47 Mn ND1 C:His386 4.31 Mn CD2 C:His386 3.25 Mn CE1 C:His386 3.34 Mn CG C:His386 4.30 Mn O3B C:Udp1 4.46 Mn PA C:Udp1 3.58 Mn O2A C:Udp1 2.37 Mn O1B C:Udp1 1.90 Mn PB C:Udp1 3.32 Mn O5' C:Udp1 4.80 Mn O2B C:Udp1 4.01 Mn O3A C:Udp1 3.85 Mn O1A C:Udp1 4.44 Mn O C:Hoh819 4.02 Mn O C:Hoh853 2.51 interactive model: Manganese binding site 6 out of 8 in 2z86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 2z86. 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: Asp519, C: Asp521, C: Asp522, C: Arg628, C: Val629, C: His631, C: Uga683, C: Hoh795, conact list: Atom Atom Distance (A) Mn CB C:Asp519 4.71 Mn OD2 C:Asp519 4.92 Mn CB C:Asp521 4.59 Mn OD2 C:Asp521 2.54 Mn OD1 C:Asp521 2.98 Mn CG C:Asp521 3.11 Mn OD2 C:Asp522 4.45 Mn OD1 C:Asp522 3.98 Mn CG C:Asp522 4.63 Mn CD C:Arg628 4.73 Mn CG C:Arg628 4.84 Mn O C:Val629 4.48 Mn NE2 C:His631 2.82 Mn ND1 C:His631 4.14 Mn CD2 C:His631 4.03 Mn CE1 C:His631 2.95 Mn CG C:His631 4.70 Mn O3B C:Uga683 4.19 Mn C5D C:Uga683 4.58 Mn PA C:Uga683 3.66 Mn C3D C:Uga683 4.94 Mn O2B C:Uga683 4.82 Mn O3A C:Uga683 4.09 Mn O5D C:Uga683 4.60 Mn O2A C:Uga683 4.72 Mn O1B C:Uga683 2.18 Mn PB C:Uga683 3.59 Mn O2' C:Uga683 4.71 Mn O1A C:Uga683 2.23 Mn O C:Hoh795 2.53 interactive model: Manganese binding site 7 out of 8 in 2z86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 2z86. 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: Arg161, D: Asp239, D: Asp241, D: His386, D: Uga683, D: Hoh796, D: Hoh807, conact list: Atom Atom Distance (A) Mn NH2 D:Arg161 4.31 Mn NH1 D:Arg161 4.82 Mn OD2 D:Asp239 4.40 Mn CB D:Asp241 4.77 Mn OD2 D:Asp241 2.52 Mn OD1 D:Asp241 3.39 Mn CG D:Asp241 3.33 Mn NE2 D:His386 2.67 Mn ND1 D:His386 3.88 Mn CD2 D:His386 3.93 Mn CE1 D:His386 2.66 Mn CG D:His386 4.53 Mn O3B D:Uga683 4.32 Mn C5D D:Uga683 4.81 Mn PA D:Uga683 3.36 Mn O5' D:Uga683 4.99 Mn O2B D:Uga683 4.69 Mn O3A D:Uga683 3.78 Mn O5D D:Uga683 4.57 Mn O2A D:Uga683 4.25 Mn O1B D:Uga683 2.12 Mn C1' D:Uga683 4.43 Mn PB D:Uga683 3.46 Mn O1A D:Uga683 2.15 Mn O D:Hoh796 4.87 Mn O D:Hoh807 2.20 interactive model: Manganese binding site 8 out of 8 in 2z86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 2z86. 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: Asp519, D: Asp521, D: Asp522, D: Arg628, D: Val629, D: His631, D: Uga684, D: Hoh756, conact list: Atom Atom Distance (A) Mn CB D:Asp519 4.70 Mn OD2 D:Asp519 4.66 Mn CB D:Asp521 4.34 Mn OD2 D:Asp521 2.38 Mn OD1 D:Asp521 2.75 Mn CG D:Asp521 2.88 Mn OD2 D:Asp522 4.17 Mn OD1 D:Asp522 4.25 Mn CG D:Asp522 4.57 Mn CD D:Arg628 4.62 Mn NE D:Arg628 4.19 Mn O D:Val629 4.23 Mn NE2 D:His631 3.80 Mn ND1 D:His631 4.55 Mn CE1 D:His631 3.35 Mn O3B D:Uga684 4.37 Mn C5D D:Uga684 4.50 Mn PA D:Uga684 3.62 Mn C3D D:Uga684 4.76 Mn O2B D:Uga684 4.81 Mn O3A D:Uga684 4.06 Mn O5D D:Uga684 4.53 Mn O2A D:Uga684 4.77 Mn O1B D:Uga684 2.28 Mn PB D:Uga684 3.66 Mn O1A D:Uga684 2.23 Mn O D:Hoh756 4.19 interactive model: