Magnesium in the structure of Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site (pdb 3tzr)

The binding sites of Magnesium atom in the structure of Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site (pdb code 3tzr). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3tzr structure was solved by S.M.DIBROV, K.DING, N.BRUNN, M.A.PARKER, B.M.BERGDAHL, D.L.WYLES, T.HERMANN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 16.8-2.2 Space group P212121 a (A) 32.054 b (A) 33.582 c (A) 81.046 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.9 Rfree (%) 23.8 Magnesium Binding Sites: Magnesium binding site 1 out of 6 in 3tzr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3tzr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A53, A: C55, A: U56, A: C58, A: U59, A: G60, B: A109, A: Hoh80, conact list: Atom Atom Distance (A) Mg N3 A:A53 4.21 Mg C2 A:A53 3.78 Mg N1 A:A53 4.75 Mg C3' A:C55 4.31 Mg C2 A:C55 4.54 Mg N1 A:C55 4.73 Mg C1' A:C55 4.53 Mg O2 A:C55 4.13 Mg O3' A:C55 4.37 Mg C2' A:C55 3.39 Mg O2' A:C55 3.55 Mg OP1 A:U56 2.60 Mg C6 A:U56 3.80 Mg C5 A:U56 3.47 Mg P A:U56 3.98 Mg C4 A:U56 4.70 Mg O5' A:U56 4.67 Mg N3 A:C58 4.89 Mg C6 A:C58 4.74 Mg C5 A:C58 3.75 Mg C4 A:C58 3.86 Mg N4 A:C58 3.50 Mg N3 A:U59 4.97 Mg C5 A:U59 4.09 Mg C4 A:U59 3.72 Mg O4 A:U59 2.76 Mg O6 A:G60 4.32 Mg N6 B:A109 4.69 Mg O A:Hoh80 2.75 interactive model: Magnesium binding site 2 out of 6 in 3tzr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3tzr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G52, A: U56, A: A57, A: C58, B: C111, B: C112, A: Mg69, A: Ss075, A: Hoh87, B: Hoh69, conact list: Atom Atom Distance (A) Mg N3 A:G52 4.06 Mg N2 A:G52 3.11 Mg C2 A:G52 3.98 Mg OP1 A:U56 4.35 Mg P A:U56 3.73 Mg OP2 A:U56 2.64 Mg C5' A:U56 3.35 Mg C4' A:U56 4.66 Mg O5' A:U56 3.97 Mg C8 A:A57 4.02 Mg C6 A:A57 3.58 Mg N1 A:A57 4.91 Mg C5 A:A57 3.50 Mg N6 A:A57 2.92 Mg N7 A:A57 2.84 Mg C4 A:A57 4.84 Mg C5 A:C58 4.66 Mg C4 A:C58 4.73 Mg N4 A:C58 4.51 Mg O2 B:C111 4.87 Mg C1' B:C112 4.84 Mg O2 B:C112 4.70 Mg MG A:Mg69 3.12 Mg C04 A:Ss075 4.99 Mg C03 A:Ss075 3.86 Mg C02 A:Ss075 4.02 Mg O A:Hoh87 3.19 Mg O B:Hoh69 4.61 interactive model: Magnesium binding site 3 out of 6 in 3tzr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3tzr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G51, A: G52, A: U56, A: A57, B: C112, A: Mg68, A: So473, A: Hoh20, A: Hoh87, B: Hoh69, conact list: Atom Atom Distance (A) Mg N2 A:G51 3.75 Mg C2 A:G51 4.73 Mg N9 A:G52 4.29 Mg N3 A:G52 2.89 Mg N2 A:G52 3.46 Mg C2 A:G52 3.59 Mg N1 A:G52 4.93 Mg C1' A:G52 3.79 Mg O4' A:G52 4.95 Mg C4 A:G52 3.94 Mg C2' A:G52 4.02 Mg O2' A:G52 3.59 Mg OP2 A:U56 5.00 Mg N7 A:A57 4.51 Mg N3 B:C112 5.00 Mg C2 B:C112 4.15 Mg N1 B:C112 4.90 Mg C1' B:C112 4.59 Mg O2 B:C112 3.03 Mg C2' B:C112 4.99 Mg O2' B:C112 4.62 Mg MG A:Mg68 3.12 Mg S A:So473 3.70 Mg O2 A:So473 3.85 Mg O4 A:So473 2.97 Mg O3 A:So473 3.73 Mg O A:Hoh20 4.58 Mg O A:Hoh87 3.06 Mg O B:Hoh69 3.06 interactive model: Magnesium binding site 4 out of 6 in 3tzr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3tzr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A53, B: G107, B: C108, B: A109, A: Ss075, A: Hoh46, B: Hoh71, conact list: Atom Atom Distance (A) Mg C8 A:A53 3.71 Mg C6 A:A53 4.67 Mg C5 A:A53 4.09 Mg N6 A:A53 4.33 Mg N7 A:A53 2.95 Mg OP1 B:G107 4.08 Mg OP1 B:C108 4.46 Mg P B:C108 4.00 Mg OP2 B:C108 2.77 Mg O5' B:C108 4.64 Mg OP2 B:A109 4.93 Mg N A:Ss075 4.08 Mg C12 A:Ss075 4.54 Mg C11 A:Ss075 3.18 Mg C05 A:Ss075 4.69 Mg C A:Ss075 3.11 Mg N02 A:Ss075 4.85 Mg C16 A:Ss075 4.26 Mg C10 A:Ss075 4.38 Mg C13 A:Ss075 4.66 Mg C09 A:Ss075 3.89 Mg N04 A:Ss075 4.43 Mg C15 A:Ss075 3.65 Mg C06 A:Ss075 4.28 Mg C08 A:Ss075 3.67 Mg O A:Hoh46 4.69 Mg O B:Hoh71 4.38 interactive model: Magnesium binding site 5 out of 6 in 3tzr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3tzr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A54, A: C55, A: Hoh83, conact list: Atom Atom Distance (A) Mg C3' A:A54 4.28 Mg C1' A:A54 4.76 Mg O3' A:A54 3.40 Mg O4' A:A54 4.14 Mg OP2 A:A54 4.39 Mg C4' A:A54 3.89 Mg C6 A:C55 4.49 Mg C5 A:C55 4.91 Mg P A:C55 4.11 Mg O4' A:C55 4.42 Mg OP2 A:C55 4.10 Mg C5' A:C55 4.12 Mg C4' A:C55 4.93 Mg O5' A:C55 3.78 Mg O A:Hoh83 2.64 interactive model: Magnesium binding site 6 out of 6 in 3tzr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3tzr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G49, B: C114, B: G115, A: Hoh8, conact list: Atom Atom Distance (A) Mg N2 A:G49 4.43 Mg C2 B:C114 4.75 Mg C1' B:C114 4.28 Mg O2 B:C114 3.67 Mg C2' B:C114 3.82 Mg O2' B:C114 2.89 Mg N9 B:G115 4.68 Mg C1' B:G115 3.97 Mg O4' B:G115 3.06 Mg C5' B:G115 4.33 Mg C4' B:G115 3.99 Mg O A:Hoh8 2.79 interactive model: