Magnesium in the structure of Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E (pdb 3gcm)

The binding sites of Magnesium atom in the structure of Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E (pdb code 3gcm). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3gcm structure was solved by S.NURMOHAMED, B.L.LUISI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.5 Space group P43212 a (A) 176.335 b (A) 176.335 c (A) 189.628 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.6 Rfree (%) 22.1 Magnesium Binding Sites: Magnesium binding site 1 out of 3 in 3gcm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3gcm. 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: Gly436, A: Ser437, A: Ala465, A: Ile481, A: Asp486, A: Asp492, A: Flc551, A: Hoh749, conact list: Atom Atom Distance (A) Mg C A:Gly436 4.49 Mg CA A:Gly436 4.06 Mg N A:Ser437 3.82 Mg CB A:Ser437 3.75 Mg OG A:Ser437 4.52 Mg CA A:Ser437 3.77 Mg CB A:Ala465 3.47 Mg CA A:Ala465 4.95 Mg O A:Ile481 4.37 Mg CD1 A:Ile481 3.79 Mg CG1 A:Ile481 3.79 Mg CB A:Asp486 4.54 Mg OD2 A:Asp486 4.32 Mg OD1 A:Asp486 4.98 Mg CG A:Asp486 4.44 Mg OD2 A:Asp492 3.17 Mg OD1 A:Asp492 3.29 Mg CG A:Asp492 3.60 Mg OB1 A:Flc551 4.89 Mg CBC A:Flc551 3.99 Mg CB A:Flc551 4.68 Mg CG A:Flc551 4.30 Mg OB2 A:Flc551 2.83 Mg O A:Hoh749 3.15 interactive model: Magnesium binding site 2 out of 3 in 3gcm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3gcm. 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: Gly436, B: Ser437, B: Ala465, B: Ile481, B: Asp486, B: Asp492, B: Lys494, B: Flc555, conact list: Atom Atom Distance (A) Mg C B:Gly436 4.41 Mg CA B:Gly436 4.05 Mg N B:Ser437 3.69 Mg CB B:Ser437 3.73 Mg OG B:Ser437 4.53 Mg CA B:Ser437 3.68 Mg CB B:Ala465 3.67 Mg O B:Ile481 4.55 Mg CD1 B:Ile481 3.82 Mg CG1 B:Ile481 3.93 Mg CB B:Asp486 4.52 Mg OD2 B:Asp486 4.40 Mg OD1 B:Asp486 4.93 Mg CG B:Asp486 4.44 Mg OD2 B:Asp492 3.10 Mg OD1 B:Asp492 3.24 Mg CG B:Asp492 3.56 Mg CE B:Lys494 4.94 Mg OB1 B:Flc555 4.63 Mg CBC B:Flc555 3.71 Mg OG2 B:Flc555 4.84 Mg CB B:Flc555 4.45 Mg CGC B:Flc555 4.90 Mg CG B:Flc555 4.16 Mg CA B:Flc555 4.81 Mg OB2 B:Flc555 2.52 interactive model: Magnesium binding site 3 out of 3 in 3gcm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3gcm. 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: Gly436, C: Ser437, C: Ala465, C: Ile481, C: Asp486, C: Asp492, C: Lys494, C: Flc552, C: Hoh573, conact list: Atom Atom Distance (A) Mg C C:Gly436 4.53 Mg CA C:Gly436 4.17 Mg N C:Ser437 3.81 Mg CB C:Ser437 3.73 Mg OG C:Ser437 4.31 Mg CA C:Ser437 3.78 Mg CB C:Ala465 3.67 Mg O C:Ile481 4.57 Mg CD1 C:Ile481 3.98 Mg CG1 C:Ile481 4.06 Mg CB C:Asp486 4.57 Mg OD2 C:Asp486 4.47 Mg OD1 C:Asp486 4.93 Mg CG C:Asp486 4.48 Mg OD2 C:Asp492 3.00 Mg OD1 C:Asp492 3.35 Mg CG C:Asp492 3.55 Mg CE C:Lys494 4.88 Mg OB1 C:Flc552 4.54 Mg CBC C:Flc552 3.63 Mg OG2 C:Flc552 4.85 Mg CB C:Flc552 4.31 Mg CGC C:Flc552 4.85 Mg CG C:Flc552 4.00 Mg CA C:Flc552 4.63 Mg OB2 C:Flc552 2.54 Mg O C:Hoh573 3.48 interactive model: