Magnesium in the structure of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed With Mg and Amppnp (pdb 1eyz)

The binding sites of Magnesium atom in the structure of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed With Mg and Amppnp (pdb code 1eyz). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1eyz structure was solved by J.B.THODEN, S.FIRESTINE, A.NIXON, S.J.BENKOVIC, H.M.HOLDEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.8 Space group P21212 a (A) 62.300 b (A) 179.500 c (A) 75.700 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Magnesium Binding Sites: Magnesium binding site 1 out of 5 in 1eyz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1eyz. 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: Glu84, A: Arg114, A: Ser159, A: Ser160, A: Glu267, A: Glu279, A: Mg402, A: Anp400, A: Hoh1119, A: Hoh1131, A: Hoh1149, A: Hoh1175, A: Hoh1229, A: Hoh1824, conact list: Atom Atom Distance (A) Mg OE1 A:Glu84 4.47 Mg OE2 A:Glu84 4.51 Mg CD A:Glu84 4.96 Mg CZ A:Arg114 4.68 Mg NH2 A:Arg114 4.41 Mg NH1 A:Arg114 4.10 Mg O A:Ser159 4.38 Mg CB A:Ser160 4.85 Mg CA A:Ser160 4.68 Mg OE1 A:Glu267 4.84 Mg OE1 A:Glu279 2.22 Mg CB A:Glu279 4.87 Mg OE2 A:Glu279 2.26 Mg CD A:Glu279 2.55 Mg CG A:Glu279 4.04 Mg MG A:Mg402 3.79 Mg PG A:Anp400 3.16 Mg O2G A:Anp400 3.61 Mg PA A:Anp400 4.50 Mg O2B A:Anp400 1.98 Mg O3A A:Anp400 4.26 Mg N3B A:Anp400 3.51 Mg O3G A:Anp400 1.92 Mg O2A A:Anp400 3.92 Mg O1B A:Anp400 4.23 Mg PB A:Anp400 3.23 Mg O1G A:Anp400 4.44 Mg O1A A:Anp400 4.65 Mg O A:Hoh1119 2.07 Mg O A:Hoh1131 2.28 Mg O A:Hoh1149 4.37 Mg O A:Hoh1175 4.01 Mg O A:Hoh1229 3.82 Mg O A:Hoh1824 4.23 interactive model: Magnesium binding site 2 out of 5 in 1eyz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1eyz. 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: Glu267, A: Glu279, A: His285, A: Mg401, A: Anp400, A: Hoh1113, A: Hoh1131, A: Hoh1143, A: Hoh1174, A: Hoh1229, A: Hoh1258, A: Hoh1331, conact list: Atom Atom Distance (A) Mg OE1 A:Glu267 2.18 Mg CB A:Glu267 4.79 Mg OE2 A:Glu267 2.11 Mg CD A:Glu267 2.46 Mg CG A:Glu267 3.97 Mg OE1 A:Glu279 2.09 Mg OE2 A:Glu279 4.18 Mg CD A:Glu279 3.10 Mg CG A:Glu279 3.71 Mg NE2 A:His285 4.76 Mg MG A:Mg401 3.79 Mg PG A:Anp400 3.21 Mg O2G A:Anp400 2.02 Mg PA A:Anp400 3.47 Mg O3' A:Anp400 4.37 Mg O5' A:Anp400 4.33 Mg O2B A:Anp400 4.02 Mg O3A A:Anp400 4.16 Mg N3B A:Anp400 3.60 Mg O3G A:Anp400 3.71 Mg O2A A:Anp400 1.97 Mg PB A:Anp400 4.18 Mg C5' A:Anp400 4.58 Mg O1G A:Anp400 4.48 Mg O1A A:Anp400 4.24 Mg O A:Hoh1113 2.16 Mg O A:Hoh1131 4.61 Mg O A:Hoh1143 4.16 Mg O A:Hoh1174 4.30 Mg O A:Hoh1229 4.19 Mg O A:Hoh1258 4.64 Mg O A:Hoh1331 4.26 interactive model: Magnesium binding site 3 out of 5 in 1eyz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1eyz. 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: Ser161, A: Asp286, A: Arg363, A: Anp400, A: Hoh1138, A: Hoh1143, A: Hoh1144, A: Hoh1173, A: Hoh1175, A: Hoh1258, A: Hoh1331, A: Hoh1394, A: Hoh1792, A: Hoh1794, conact list: Atom Atom Distance (A) Mg N A:Ser161 4.93 Mg CB A:Ser161 4.87 Mg OG A:Ser161 4.01 Mg CA A:Ser161 4.77 Mg CB A:Asp286 4.52 Mg OD2 A:Asp286 2.60 Mg OD1 A:Asp286 3.28 Mg CG A:Asp286 3.23 Mg NH2 A:Arg363 4.63 Mg PG A:Anp400 3.38 Mg O2G A:Anp400 3.47 Mg N3B A:Anp400 4.56 Mg O3G A:Anp400 4.36 Mg O1G A:Anp400 2.30 Mg O A:Hoh1138 4.79 Mg O A:Hoh1143 2.14 Mg O A:Hoh1144 3.77 Mg O A:Hoh1173 4.45 Mg O A:Hoh1175 4.16 Mg O A:Hoh1258 2.97 Mg O A:Hoh1331 4.34 Mg O A:Hoh1394 3.55 Mg O A:Hoh1792 2.23 Mg O A:Hoh1794 2.28 interactive model: Magnesium binding site 4 out of 5 in 1eyz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1eyz. 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: Glu84, B: Arg114, B: Ser159, B: Ser160, B: Glu279, B: Mg402, B: Anp961, B: Hoh1505, B: Hoh1528, B: Hoh1542, B: Hoh1615, B: Hoh1626, B: Hoh1661, B: Hoh1885, conact list: Atom Atom Distance (A) Mg OE1 B:Glu84 3.77 Mg CD B:Glu84 4.88 Mg CZ B:Arg114 4.31 Mg NH2 B:Arg114 3.81 Mg NH1 B:Arg114 4.08 Mg O B:Ser159 4.26 Mg CB B:Ser160 4.89 Mg CA B:Ser160 4.82 Mg OE1 B:Glu279 2.37 Mg CB B:Glu279 4.90 Mg OE2 B:Glu279 2.23 Mg CD B:Glu279 2.62 Mg CG B:Glu279 4.13 Mg MG B:Mg402 3.91 Mg PG B:Anp961 3.34 Mg O2G B:Anp961 3.91 Mg PA B:Anp961 4.55 Mg O2B B:Anp961 1.96 Mg O3A B:Anp961 4.16 Mg N3B B:Anp961 3.69 Mg O3G B:Anp961 2.00 Mg O2A B:Anp961 4.08 Mg O1B B:Anp961 4.28 Mg PB B:Anp961 3.28 Mg O1G B:Anp961 4.51 Mg O1A B:Anp961 4.73 Mg O B:Hoh1505 4.90 Mg O B:Hoh1528 4.56 Mg O B:Hoh1542 3.79 Mg O B:Hoh1615 1.88 Mg O B:Hoh1626 3.77 Mg O B:Hoh1661 4.19 Mg O B:Hoh1885 2.47 interactive model: Magnesium binding site 5 out of 5 in 1eyz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 1eyz. 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: Glu267, B: Glu279, B: His285, B: Mg401, B: Anp961, B: Hoh1473, B: Hoh1542, B: Hoh1555, B: Hoh1579, B: Hoh1885, B: Hoh2064, conact list: Atom Atom Distance (A) Mg OE1 B:Glu267 2.45 Mg CB B:Glu267 4.92 Mg OE2 B:Glu267 2.14 Mg CD B:Glu267 2.62 Mg CG B:Glu267 4.14 Mg OE1 B:Glu279 2.00 Mg OE2 B:Glu279 4.18 Mg CD B:Glu279 3.08 Mg CG B:Glu279 3.72 Mg NE2 B:His285 4.79 Mg MG B:Mg401 3.91 Mg PG B:Anp961 2.97 Mg O2G B:Anp961 1.81 Mg PA B:Anp961 3.43 Mg O3' B:Anp961 4.39 Mg O5' B:Anp961 4.29 Mg O2B B:Anp961 4.14 Mg O3A B:Anp961 4.08 Mg N3B B:Anp961 3.45 Mg C3' B:Anp961 4.83 Mg O3G B:Anp961 3.45 Mg O2A B:Anp961 1.97 Mg PB B:Anp961 4.12 Mg C5' B:Anp961 4.38 Mg O1G B:Anp961 4.21 Mg O1A B:Anp961 4.29 Mg O B:Hoh1473 2.04 Mg O B:Hoh1542 3.83 Mg O B:Hoh1555 4.28 Mg O B:Hoh1579 4.99 Mg O B:Hoh1885 4.87 Mg O B:Hoh2064 4.08 interactive model: