Magnesium in the structure of Crystal Structure of Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus With Quinupristin (pdb 2z2p)

The binding sites of Magnesium atom in the structure of Crystal Structure of Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus With Quinupristin (pdb code 2z2p). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2z2p structure was solved by M.KORCZYNSKA, A.M.BERGHUIS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.2-2.8 Space group P212121 a (A) 70.999 b (A) 93.700 c (A) 95.301 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 26.2 Rfree (%) 31.8 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 2z2p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2z2p. 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: Trp243, A: Glu268, A: Glu284, C: Mhw1, C: Thr2, A: Dol2002, conact list: Atom Atom Distance (A) Mg CZ2 A:Trp243 4.75 Mg CE2 A:Trp243 4.84 Mg NE1 A:Trp243 4.24 Mg OE1 A:Glu268 2.07 Mg CB A:Glu268 4.64 Mg OE2 A:Glu268 3.60 Mg CD A:Glu268 3.11 Mg CG A:Glu268 4.33 Mg OE1 A:Glu284 1.90 Mg CB A:Glu284 4.64 Mg OE2 A:Glu284 3.39 Mg CD A:Glu284 2.97 Mg CG A:Glu284 4.27 Mg O C:Mhw1 1.93 Mg N C:Mhw1 4.68 Mg CB C:Mhw1 2.84 Mg CG2 C:Mhw1 4.04 Mg OG1 C:Mhw1 1.71 Mg C C:Mhw1 2.93 Mg CA C:Mhw1 3.32 Mg N C:Thr2 4.14 Mg CA C:Thr2 4.75 Mg O40 A:Dol2002 4.95 interactive model: Magnesium binding site 2 out of 4 in 2z2p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2z2p. 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: Ser65, A: Asp67, A: Glu69, A: Trp71, A: Arg82, A: Asp127, conact list: Atom Atom Distance (A) Mg CB A:Ser65 4.72 Mg OG A:Ser65 4.00 Mg CB A:Asp67 4.56 Mg OD2 A:Asp67 2.51 Mg OD1 A:Asp67 3.04 Mg CG A:Asp67 3.11 Mg OE1 A:Glu69 4.03 Mg CB A:Glu69 4.41 Mg OE2 A:Glu69 1.98 Mg CD A:Glu69 3.22 Mg CG A:Glu69 4.17 Mg CD1 A:Trp71 4.90 Mg CZ2 A:Trp71 3.96 Mg CE2 A:Trp71 4.19 Mg NE1 A:Trp71 3.69 Mg CZ A:Arg82 4.66 Mg NE A:Arg82 4.66 Mg NH2 A:Arg82 4.10 Mg CB A:Asp127 4.08 Mg OD2 A:Asp127 2.14 Mg OD1 A:Asp127 2.42 Mg CG A:Asp127 2.59 Mg CA A:Asp127 4.77 interactive model: Magnesium binding site 3 out of 4 in 2z2p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2z2p. 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: Trp243, B: Glu268, B: Glu284, D: Mhw1, D: Thr2, B: Dol2003, conact list: Atom Atom Distance (A) Mg CZ2 B:Trp243 4.83 Mg CE2 B:Trp243 4.93 Mg NE1 B:Trp243 4.31 Mg OE1 B:Glu268 2.09 Mg CB B:Glu268 4.68 Mg OE2 B:Glu268 3.28 Mg CD B:Glu268 3.00 Mg CG B:Glu268 4.33 Mg OE1 B:Glu284 1.95 Mg CB B:Glu284 4.67 Mg OE2 B:Glu284 3.44 Mg CD B:Glu284 3.01 Mg CG B:Glu284 4.31 Mg O D:Mhw1 2.08 Mg N D:Mhw1 4.75 Mg CB D:Mhw1 2.84 Mg CG2 D:Mhw1 4.01 Mg OG1 D:Mhw1 1.66 Mg C D:Mhw1 3.07 Mg CA D:Mhw1 3.40 Mg N D:Thr2 4.29 Mg CA D:Thr2 4.86 Mg O41 B:Dol2003 4.64 interactive model: Magnesium binding site 4 out of 4 in 2z2p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2z2p. 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: Ser65, B: Asp67, B: Glu69, B: Trp71, B: Asp127, conact list: Atom Atom Distance (A) Mg CB B:Ser65 4.78 Mg OG B:Ser65 4.14 Mg CB B:Asp67 4.48 Mg OD2 B:Asp67 2.50 Mg OD1 B:Asp67 3.14 Mg CG B:Asp67 3.11 Mg OE1 B:Glu69 3.75 Mg CB B:Glu69 4.60 Mg OE2 B:Glu69 1.91 Mg CD B:Glu69 3.09 Mg CG B:Glu69 4.19 Mg CZ2 B:Trp71 4.18 Mg CE2 B:Trp71 4.38 Mg NE1 B:Trp71 3.83 Mg CB B:Asp127 4.04 Mg OD2 B:Asp127 2.09 Mg OD1 B:Asp127 2.37 Mg CG B:Asp127 2.54 Mg CA B:Asp127 4.73 interactive model: