Magnesium in the structure of A New Pii Protein Structure (pdb 3mhy)

The binding sites of Magnesium atom in the structure of A New Pii Protein Structure (pdb code 3mhy). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3mhy structure was solved by F.K.WINKLER, D.TRUAN, X.D.LI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.4 Space group C2221 a (A) 64.980 b (A) 87.950 c (A) 116.880 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16 Rfree (%) 19.8 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 3mhy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3mhy. 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: Gly37, A: Arg38, A: Gln39, A: Ile86, A: Gly87, A: Atp113, A: Akg114, A: Hoh134, conact list: Atom Atom Distance (A) Mg N A:Gly37 4.57 Mg C A:Gly37 4.35 Mg CA A:Gly37 4.17 Mg N A:Arg38 3.93 Mg CB A:Arg38 4.88 Mg C A:Arg38 4.97 Mg CA A:Arg38 4.79 Mg NE2 A:Gln39 3.94 Mg N A:Gln39 4.13 Mg OE1 A:Gln39 2.02 Mg CB A:Gln39 4.38 Mg CD A:Gln39 3.22 Mg CG A:Gln39 4.35 Mg CA A:Gln39 4.89 Mg CB A:Ile86 4.40 Mg C A:Ile86 4.63 Mg CA A:Ile86 4.85 Mg N A:Gly87 3.82 Mg CA A:Gly87 4.19 Mg PG A:Atp113 3.22 Mg O3B A:Atp113 3.51 Mg O2G A:Atp113 2.03 Mg PA A:Atp113 3.28 Mg O5' A:Atp113 4.48 Mg O2B A:Atp113 4.51 Mg O3A A:Atp113 3.53 Mg O3G A:Atp113 4.46 Mg O2A A:Atp113 4.14 Mg O1B A:Atp113 2.08 Mg PB A:Atp113 3.15 Mg O1G A:Atp113 3.76 Mg O1A A:Atp113 2.07 Mg O5 A:Akg114 2.15 Mg O2 A:Akg114 2.06 Mg C4 A:Akg114 4.90 Mg C1 A:Akg114 2.78 Mg O1 A:Akg114 4.00 Mg C3 A:Akg114 4.29 Mg C2 A:Akg114 2.81 Mg O A:Hoh134 3.99 interactive model: Magnesium binding site 2 out of 4 in 3mhy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3mhy. 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: Asp95, C: Asp95, A: Hoh117, A: Hoh119, A: Hoh120, A: Hoh225, B: Hoh119, B: Hoh212, C: Hoh116, C: Hoh117, C: Hoh248, conact list: Atom Atom Distance (A) Mg CB A:Asp95 4.94 Mg OD2 A:Asp95 4.19 Mg CG A:Asp95 4.97 Mg OD2 C:Asp95 4.67 Mg O A:Hoh117 2.14 Mg O A:Hoh119 2.14 Mg O A:Hoh120 2.12 Mg O A:Hoh225 4.52 Mg O B:Hoh119 4.99 Mg O B:Hoh212 4.07 Mg O C:Hoh116 2.16 Mg O C:Hoh117 2.16 Mg O C:Hoh248 3.47 interactive model: Magnesium binding site 3 out of 4 in 3mhy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3mhy. 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: B: Gly37, B: Arg38, B: Gln39, B: Ile86, B: Gly87, B: Atp113, B: Akg114, B: Hoh130, conact list: Atom Atom Distance (A) Mg N B:Gly37 4.53 Mg C B:Gly37 4.35 Mg CA B:Gly37 4.13 Mg N B:Arg38 4.02 Mg CG B:Arg38 4.64 Mg CA B:Arg38 4.98 Mg NE2 B:Gln39 3.94 Mg N B:Gln39 4.20 Mg OE1 B:Gln39 2.08 Mg CB B:Gln39 4.43 Mg CD B:Gln39 3.26 Mg CG B:Gln39 4.41 Mg CA B:Gln39 4.94 Mg CB B:Ile86 4.40 Mg C B:Ile86 4.55 Mg CA B:Ile86 4.76 Mg N B:Gly87 3.70 Mg CA B:Gly87 4.11 Mg PG B:Atp113 3.23 Mg O3B B:Atp113 3.51 Mg O2G B:Atp113 2.02 Mg PA B:Atp113 3.27 Mg O5' B:Atp113 4.45 Mg O2B B:Atp113 2.04 Mg O3A B:Atp113 3.54 Mg O3G B:Atp113 3.79 Mg O2A B:Atp113 2.08 Mg O1B B:Atp113 4.49 Mg PB B:Atp113 3.13 Mg O1G B:Atp113 4.46 Mg O1A B:Atp113 4.15 Mg O5 B:Akg114 2.16 Mg O2 B:Akg114 2.03 Mg C4 B:Akg114 4.91 Mg C1 B:Akg114 2.79 Mg O1 B:Akg114 4.01 Mg C3 B:Akg114 4.31 Mg O4 B:Akg114 4.96 Mg C2 B:Akg114 2.83 Mg O B:Hoh130 4.00 interactive model: Magnesium binding site 4 out of 4 in 3mhy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3mhy. 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: C: Gly37, C: Arg38, C: Gln39, C: Ile86, C: Gly87, C: Atp113, C: Akg114, C: Hoh129, conact list: Atom Atom Distance (A) Mg N C:Gly37 4.50 Mg C C:Gly37 4.34 Mg CA C:Gly37 4.09 Mg N C:Arg38 3.99 Mg CG C:Arg38 4.59 Mg CA C:Arg38 4.96 Mg NE2 C:Gln39 3.91 Mg N C:Gln39 4.20 Mg OE1 C:Gln39 2.04 Mg CB C:Gln39 4.39 Mg CD C:Gln39 3.22 Mg CG C:Gln39 4.37 Mg CA C:Gln39 4.93 Mg CB C:Ile86 4.49 Mg C C:Ile86 4.60 Mg CA C:Ile86 4.84 Mg N C:Gly87 3.73 Mg CA C:Gly87 4.10 Mg PG C:Atp113 3.22 Mg O3B C:Atp113 3.50 Mg O2G C:Atp113 4.46 Mg PA C:Atp113 3.30 Mg O5' C:Atp113 4.47 Mg O2B C:Atp113 4.51 Mg O3A C:Atp113 3.55 Mg O3G C:Atp113 3.79 Mg O2A C:Atp113 4.18 Mg O1B C:Atp113 2.06 Mg PB C:Atp113 3.16 Mg O1G C:Atp113 2.02 Mg O1A C:Atp113 2.08 Mg O5 C:Akg114 2.14 Mg O2 C:Akg114 2.04 Mg C4 C:Akg114 4.91 Mg C1 C:Akg114 2.77 Mg O1 C:Akg114 3.98 Mg C3 C:Akg114 4.30 Mg O3 C:Akg114 5.00 Mg C2 C:Akg114 2.81 Mg O C:Hoh129 4.05 interactive model: