Magnesium in the structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex With Mg-Amppcp (pdb 1kji)

The binding sites of Magnesium atom in the structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex With Mg-Amppcp (pdb code 1kji). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1kji structure was solved by J.B.THODEN, S.M.FIRESTINE, S.J.BENKOVIC, H.M.HOLDEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.6 Space group P21212 a (A) 62.200 b (A) 179.200 c (A) 76.200 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1kji Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1kji. 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: Mg394, A: Acp1, A: Hoh466, A: Hoh501, A: Hoh509, A: Hoh536, A: Hoh644, A: Hoh739, conact list: Atom Atom Distance (A) Mg OE1 A:Glu84 4.37 Mg OE2 A:Glu84 4.50 Mg CD A:Glu84 4.76 Mg CZ A:Arg114 4.57 Mg NH2 A:Arg114 4.34 Mg NH1 A:Arg114 4.05 Mg O A:Ser159 4.12 Mg CB A:Ser160 4.90 Mg CA A:Ser160 4.68 Mg OE1 A:Glu267 5.00 Mg OE1 A:Glu279 2.38 Mg CB A:Glu279 4.98 Mg OE2 A:Glu279 2.46 Mg CD A:Glu279 2.73 Mg CG A:Glu279 4.21 Mg MG A:Mg394 3.95 Mg PG A:Acp1 3.23 Mg O2G A:Acp1 3.77 Mg PA A:Acp1 4.73 Mg O2B A:Acp1 1.96 Mg O3A A:Acp1 4.35 Mg O3G A:Acp1 2.05 Mg O2A A:Acp1 4.29 Mg O1B A:Acp1 4.06 Mg C3B A:Acp1 3.62 Mg PB A:Acp1 3.21 Mg O1G A:Acp1 4.48 Mg O1A A:Acp1 4.80 Mg O A:Hoh466 4.44 Mg O A:Hoh501 3.84 Mg O A:Hoh509 1.84 Mg O A:Hoh536 2.54 Mg O A:Hoh644 4.31 Mg O A:Hoh739 4.89 interactive model: Magnesium binding site 2 out of 4 in 1kji Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1kji. 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: Mg393, A: Acp1, A: Hoh465, A: Hoh501, A: Hoh516, A: Hoh536, A: Hoh563, A: Hoh592, conact list: Atom Atom Distance (A) Mg OE1 A:Glu267 2.24 Mg CB A:Glu267 4.91 Mg OE2 A:Glu267 2.36 Mg CD A:Glu267 2.64 Mg CG A:Glu267 4.16 Mg OE1 A:Glu279 2.12 Mg OE2 A:Glu279 4.23 Mg CD A:Glu279 3.15 Mg CG A:Glu279 3.82 Mg NE2 A:His285 4.67 Mg MG A:Mg393 3.95 Mg PG A:Acp1 3.21 Mg O2G A:Acp1 2.10 Mg PA A:Acp1 3.50 Mg O3' A:Acp1 4.50 Mg O5' A:Acp1 4.40 Mg O2B A:Acp1 3.87 Mg O3A A:Acp1 4.05 Mg O3G A:Acp1 3.79 Mg O2A A:Acp1 2.08 Mg C3B A:Acp1 3.49 Mg PB A:Acp1 3.99 Mg C5' A:Acp1 4.49 Mg O1G A:Acp1 4.45 Mg O1A A:Acp1 4.31 Mg O A:Hoh465 2.20 Mg O A:Hoh501 4.03 Mg O A:Hoh516 4.23 Mg O A:Hoh536 4.96 Mg O A:Hoh563 3.80 Mg O A:Hoh592 4.13 interactive model: Magnesium binding site 3 out of 4 in 1kji Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1kji. 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: Glu267, B: Glu279, B: Mg394, B: Acp396, B: Hoh470, B: Hoh491, B: Hoh520, B: Hoh526, B: Hoh547, B: Hoh557, conact list: Atom Atom Distance (A) Mg OE1 B:Glu84 4.80 Mg OE2 B:Glu84 4.42 Mg CD B:Glu84 4.98 Mg CZ B:Arg114 4.46 Mg NH2 B:Arg114 4.18 Mg NH1 B:Arg114 4.07 Mg O B:Ser159 4.30 Mg CB B:Ser160 4.91 Mg CA B:Ser160 4.82 Mg OE1 B:Glu267 4.85 Mg OE1 B:Glu279 2.11 Mg CB B:Glu279 4.80 Mg OE2 B:Glu279 2.27 Mg CD B:Glu279 2.49 Mg CG B:Glu279 3.99 Mg MG B:Mg394 3.78 Mg PG B:Acp396 3.21 Mg O2G B:Acp396 3.53 Mg PA B:Acp396 4.43 Mg O2B B:Acp396 2.05 Mg O3A B:Acp396 4.18 Mg O3G B:Acp396 2.10 Mg O2A B:Acp396 4.00 Mg O1B B:Acp396 4.36 Mg C3B B:Acp396 3.70 Mg PB B:Acp396 3.30 Mg O1G B:Acp396 4.49 Mg O1A B:Acp396 4.55 Mg O B:Hoh470 2.85 Mg O B:Hoh491 4.92 Mg O B:Hoh520 4.23 Mg O B:Hoh526 3.94 Mg O B:Hoh547 1.71 Mg O B:Hoh557 4.56 interactive model: Magnesium binding site 4 out of 4 in 1kji Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1kji. 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: Mg393, B: Acp396, B: Hoh503, B: Hoh526, B: Hoh635, conact list: Atom Atom Distance (A) Mg OE1 B:Glu267 2.81 Mg OE2 B:Glu267 2.29 Mg CD B:Glu267 2.91 Mg CG B:Glu267 4.37 Mg OE1 B:Glu279 2.27 Mg OE2 B:Glu279 4.29 Mg CD B:Glu279 3.22 Mg CG B:Glu279 3.80 Mg MG B:Mg393 3.78 Mg PG B:Acp396 3.20 Mg O2G B:Acp396 1.90 Mg PA B:Acp396 3.17 Mg O3' B:Acp396 4.36 Mg O5' B:Acp396 4.04 Mg O2B B:Acp396 3.97 Mg O3A B:Acp396 3.60 Mg C3' B:Acp396 4.77 Mg O3G B:Acp396 3.84 Mg O2A B:Acp396 1.85 Mg C3B B:Acp396 3.68 Mg PB B:Acp396 3.91 Mg C5' B:Acp396 4.13 Mg O1G B:Acp396 4.35 Mg O1A B:Acp396 4.21 Mg O B:Hoh503 3.92 Mg O B:Hoh526 4.30 Mg O B:Hoh635 2.45 interactive model: