Magnesium in the structure of Crystal Structure of Staphylococcus Aureus Membrane-Bound Transglycosylase in Complex With A Lipid II Analog (pdb 3vmt)

The binding sites of Magnesium atom in the structure of Crystal Structure of Staphylococcus Aureus Membrane-Bound Transglycosylase in Complex With A Lipid II Analog (pdb code 3vmt). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3vmt structure was solved by C.Y.HUANG, H.W.SHIH, L.Y.LIN, Y.W.TIEN, T.J.R.CHENG, W.C.CHENG, C.H.WONG, C.MA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.1-2.3 Space group P212121 a (A) 66.493 b (A) 67.429 c (A) 152.186 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.7 Rfree (%) 24.2 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 3vmt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3vmt. 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: Ser98, A: Met99, A: Glu100, A: Glu102, A: Lys248, A: Gln252, A: Lhi301, A: Hoh401, conact list: Atom Atom Distance (A) Mg O A:Ser98 2.35 Mg C A:Ser98 3.57 Mg CA A:Ser98 4.60 Mg O A:Met99 4.09 Mg N A:Met99 4.39 Mg C A:Met99 4.26 Mg CA A:Met99 4.32 Mg N A:Glu100 4.97 Mg N A:Glu102 4.86 Mg OE1 A:Glu102 2.36 Mg CB A:Glu102 4.16 Mg OE2 A:Glu102 4.53 Mg CD A:Glu102 3.41 Mg CG A:Glu102 3.81 Mg CE A:Lys248 3.93 Mg CD A:Lys248 3.45 Mg CG A:Lys248 4.72 Mg NZ A:Lys248 3.31 Mg OE1 A:Gln252 4.21 Mg OA2 A:Lhi301 2.73 Mg C11 A:Lhi301 3.74 Mg C8 A:Lhi301 3.95 Mg C13 A:Lhi301 3.77 Mg C10 A:Lhi301 4.02 Mg OB3 A:Lhi301 4.60 Mg OA9 A:Lhi301 2.81 Mg C9 A:Lhi301 4.24 Mg C12 A:Lhi301 3.53 Mg OA3 A:Lhi301 4.97 Mg O A:Hoh401 4.55 interactive model: Magnesium binding site 2 out of 2 in 3vmt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3vmt. 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: Gly109, A: Phe110, A: Asp111, A: Thr115, A: Gly131, A: Ser132, A: Thr133, A: Gln136, A: Lhi301, conact list: Atom Atom Distance (A) Mg O A:Gly109 4.57 Mg CB A:Phe110 4.88 Mg CD1 A:Phe110 4.03 Mg C A:Phe110 4.22 Mg CE1 A:Phe110 4.41 Mg CG A:Phe110 4.54 Mg CA A:Phe110 4.14 Mg O A:Asp111 3.61 Mg N A:Asp111 3.37 Mg CB A:Asp111 4.34 Mg C A:Asp111 4.23 Mg CA A:Asp111 4.16 Mg N A:Thr115 4.75 Mg CB A:Thr115 3.77 Mg CG2 A:Thr115 4.53 Mg OG1 A:Thr115 2.34 Mg CA A:Thr115 4.60 Mg O A:Gly131 2.98 Mg C A:Gly131 4.12 Mg N A:Ser132 4.69 Mg C A:Ser132 4.55 Mg CA A:Ser132 4.27 Mg N A:Thr133 3.85 Mg CB A:Thr133 4.31 Mg CG2 A:Thr133 4.80 Mg CA A:Thr133 4.69 Mg NE2 A:Gln136 3.63 Mg OE1 A:Gln136 2.35 Mg CD A:Gln136 3.33 Mg CG A:Gln136 4.72 Mg CA1 A:Lhi301 4.21 interactive model: