Magnesium in the structure of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase With Xmp, Pyrophosphate and Two MG2+ Ions (pdb 1qk5)

The binding sites of Magnesium atom in the structure of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase With Xmp, Pyrophosphate and Two MG2+ Ions (pdb code 1qk5). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1qk5 structure was solved by A.HEROUX, E.L.WHITE, L.J.ROSS, R.L.DAVIS, D.W.BORHANI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 13.0-1.6 Space group C2221 a (A) 55.208 b (A) 112.255 c (A) 144.280 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.351 Rfree (%) 26.099 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1qk5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1qk5. 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: Ile77, A: Leu78, A: Lys79, A: Gly80, A: Leu115, A: Glu146, A: Asp147, A: Xmp300, A: Pop301, A: Mg303, A: Hoh2062, A: Hoh2065, A: Hoh2098, A: Hoh2099, A: Hoh2102, conact list: Atom Atom Distance (A) Mg CG2 A:Ile77 4.86 Mg O A:Leu78 4.74 Mg N A:Lys79 4.93 Mg N A:Gly80 4.23 Mg CA A:Gly80 4.39 Mg O A:Leu115 4.66 Mg OE1 A:Glu146 4.45 Mg OE2 A:Glu146 4.27 Mg CD A:Glu146 4.78 Mg OD2 A:Asp147 4.04 Mg OD1 A:Asp147 3.95 Mg CG A:Asp147 4.45 Mg C3' A:Xmp300 4.37 Mg C1' A:Xmp300 4.90 Mg O3' A:Xmp300 3.45 Mg C2' A:Xmp300 4.33 Mg O2' A:Xmp300 3.28 Mg O A:Pop301 3.32 Mg O5 A:Pop301 3.92 Mg P2 A:Pop301 3.17 Mg O2 A:Pop301 3.81 Mg P1 A:Pop301 3.19 Mg O1 A:Pop301 2.06 Mg O3 A:Pop301 4.43 Mg O4 A:Pop301 2.09 Mg O6 A:Pop301 4.30 Mg MG A:Mg303 4.78 Mg O A:Hoh2062 2.38 Mg O A:Hoh2065 2.26 Mg O A:Hoh2098 4.04 Mg O A:Hoh2099 2.16 Mg O A:Hoh2102 4.01 interactive model: Magnesium binding site 2 out of 4 in 1qk5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1qk5. 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: Asp206, A: Arg212, A: Xmp300, A: Pop301, A: Mg302, A: Hoh2082, A: Hoh2083, A: Hoh2084, A: Hoh2085, A: Hoh2086, A: Hoh2102, conact list: Atom Atom Distance (A) Mg O A:Asp206 4.66 Mg N A:Asp206 4.71 Mg CB A:Asp206 4.51 Mg OD2 A:Asp206 3.29 Mg OD1 A:Asp206 2.13 Mg CG A:Asp206 3.15 Mg CZ A:Arg212 4.55 Mg NH2 A:Arg212 3.97 Mg NH1 A:Arg212 4.25 Mg N3 A:Xmp300 4.47 Mg C2 A:Xmp300 4.85 Mg O2 A:Xmp300 4.35 Mg O A:Pop301 3.39 Mg O5 A:Pop301 2.09 Mg P2 A:Pop301 3.30 Mg O2 A:Pop301 2.36 Mg P1 A:Pop301 3.28 Mg O1 A:Pop301 4.26 Mg O3 A:Pop301 4.28 Mg O4 A:Pop301 4.18 Mg O6 A:Pop301 4.38 Mg MG A:Mg302 4.78 Mg O A:Hoh2082 4.04 Mg O A:Hoh2083 2.23 Mg O A:Hoh2084 2.02 Mg O A:Hoh2085 4.49 Mg O A:Hoh2086 4.92 Mg O A:Hoh2102 2.16 interactive model: Magnesium binding site 3 out of 4 in 1qk5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1qk5. 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: Ile77, B: Leu78, B: Lys79, B: Gly80, B: Leu115, B: Glu146, B: Asp147, B: Xmp300, B: Pop301, B: Mg303, B: Hoh2049, B: Hoh2053, B: Hoh2054, B: Hoh2077, B: Hoh2078, B: Hoh2079, conact list: Atom Atom Distance (A) Mg O B:Ile77 4.74 Mg CG2 B:Ile77 4.51 Mg O B:Leu78 4.32 Mg C B:Leu78 4.76 Mg N B:Lys79 4.81 Mg N B:Gly80 4.25 Mg CA B:Gly80 4.51 Mg O B:Leu115 4.40 Mg OE1 B:Glu146 4.67 Mg OE2 B:Glu146 4.17 Mg CD B:Glu146 4.83 Mg OD2 B:Asp147 4.34 Mg OD1 B:Asp147 4.23 Mg CG B:Asp147 4.75 Mg C3' B:Xmp300 4.67 Mg O3' B:Xmp300 3.74 Mg C2' B:Xmp300 4.81 Mg O2' B:Xmp300 3.86 Mg O B:Pop301 3.40 Mg O5 B:Pop301 4.24 Mg P2 B:Pop301 3.24 Mg O2 B:Pop301 4.17 Mg P1 B:Pop301 3.22 Mg O1 B:Pop301 2.09 Mg O3 B:Pop301 4.34 Mg O4 B:Pop301 2.24 Mg O6 B:Pop301 4.34 Mg MG B:Mg303 4.86 Mg O B:Hoh2049 2.14 Mg O B:Hoh2053 2.25 Mg O B:Hoh2054 2.24 Mg O B:Hoh2077 2.08 Mg O B:Hoh2078 4.18 Mg O B:Hoh2079 3.89 interactive model: Magnesium binding site 4 out of 4 in 1qk5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1qk5. 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: Asp206, B: Arg212, B: Xmp300, B: Pop301, B: Mg302, B: Hoh2055, B: Hoh2063, B: Hoh2064, B: Hoh2077, B: Hoh2078, B: Hoh2080, conact list: Atom Atom Distance (A) Mg O B:Asp206 4.88 Mg N B:Asp206 4.81 Mg CB B:Asp206 4.66 Mg OD2 B:Asp206 3.54 Mg OD1 B:Asp206 2.25 Mg CG B:Asp206 3.29 Mg CZ B:Arg212 4.67 Mg NH2 B:Arg212 4.06 Mg NH1 B:Arg212 4.25 Mg N3 B:Xmp300 4.44 Mg C2 B:Xmp300 4.94 Mg O2 B:Xmp300 4.45 Mg O B:Pop301 3.23 Mg O5 B:Pop301 2.00 Mg P2 B:Pop301 3.13 Mg O2 B:Pop301 2.31 Mg P1 B:Pop301 3.20 Mg O1 B:Pop301 4.06 Mg O3 B:Pop301 4.32 Mg O4 B:Pop301 4.00 Mg O6 B:Pop301 4.22 Mg MG B:Mg302 4.86 Mg O B:Hoh2055 4.07 Mg O B:Hoh2063 2.40 Mg O B:Hoh2064 2.30 Mg O B:Hoh2077 4.27 Mg O B:Hoh2078 2.29 Mg O B:Hoh2080 4.89 interactive model: