Magnesium in the structure of Structure of NUDT9 Complexed With Ribose-5-Phosphate (pdb 1qvj)

The binding sites of Magnesium atom in the structure of Structure of NUDT9 Complexed With Ribose-5-Phosphate (pdb code 1qvj). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1qvj structure was solved by B.W.SHEN, A.-L.PERRAUD, A.S.SCHARENBERG, B.L.STODDARD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 42.0-1.9 Space group I222 a (A) 78.900 b (A) 87.455 c (A) 120.308 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.2 Rfree (%) 24.2 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 1qvj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1qvj. 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: Arg204, A: Gly214, A: Gly215, A: Glu230, A: Mg561, A: Rp5554, A: Hoh428, A: Hoh443, A: Hoh458, A: Hoh492, A: Hoh549, conact list: Atom Atom Distance (A) Mg NH1 A:Arg204 4.37 Mg O A:Gly214 2.90 Mg C A:Gly214 3.96 Mg N A:Gly215 4.43 Mg CA A:Gly215 3.94 Mg OE1 A:Glu230 4.59 Mg MG A:Mg561 3.52 Mg O1X A:Rp5554 4.64 Mg O2X A:Rp5554 4.09 Mg O3X A:Rp5554 2.75 Mg P' A:Rp5554 4.00 Mg O A:Hoh428 3.57 Mg O A:Hoh443 2.71 Mg O A:Hoh458 4.16 Mg O A:Hoh492 4.08 Mg O A:Hoh549 2.92 interactive model: Magnesium binding site 2 out of 2 in 1qvj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1qvj. 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: Gly214, A: Gly215, A: Mse216, A: Arg229, A: Glu230, A: Asp305, A: Mg560, A: Rp5554, A: Hoh443, A: Hoh445, A: Hoh492, A: Hoh514, A: Hoh531, conact list: Atom Atom Distance (A) Mg O A:Gly214 4.44 Mg C A:Gly215 4.78 Mg CA A:Gly215 4.04 Mg N A:Mse216 4.50 Mg NH1 A:Arg229 4.92 Mg OE1 A:Glu230 3.20 Mg OE2 A:Glu230 2.97 Mg CD A:Glu230 3.35 Mg CG A:Glu230 4.66 Mg OD2 A:Asp305 4.78 Mg MG A:Mg560 3.52 Mg O3X A:Rp5554 4.69 Mg O A:Hoh443 2.88 Mg O A:Hoh445 2.88 Mg O A:Hoh492 4.81 Mg O A:Hoh514 2.80 Mg O A:Hoh531 4.21 interactive model: