Magnesium in the structure of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed With 2 Gmp, 1 Mg Per Subunit (pdb 1ecb)

The binding sites of Magnesium atom in the structure of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed With 2 Gmp, 1 Mg Per Subunit (pdb code 1ecb). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1ecb structure was solved by J.M.KRAHN, J.L.SMITH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-2.7 Space group P212121 a (A) 95.800 b (A) 113.200 c (A) 199.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.8 Rfree (%) 29.1 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1ecb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1ecb. 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: Tyr258, A: Ile301, A: Pro302, A: Asp366, A: Asp367, A: Ser368, A: 5gp505, A: 5gp506, A: Hoh508, A: Hoh509, conact list: Atom Atom Distance (A) Mg CE1 A:Tyr258 4.89 Mg O A:Ile301 4.51 Mg CG2 A:Ile301 4.65 Mg O A:Pro302 4.86 Mg CB A:Asp366 4.58 Mg OD2 A:Asp366 3.61 Mg C A:Asp366 4.90 Mg OD1 A:Asp366 2.29 Mg CG A:Asp366 3.26 Mg CA A:Asp366 4.87 Mg N A:Asp367 4.07 Mg CB A:Asp367 4.33 Mg OD2 A:Asp367 3.55 Mg OD1 A:Asp367 2.09 Mg CG A:Asp367 3.10 Mg CA A:Asp367 4.70 Mg O A:Ser368 4.77 Mg N A:Ser368 4.78 Mg C3' A:5gp505 2.82 Mg C1' A:5gp505 3.86 Mg O4' A:5gp505 4.22 Mg O3' A:5gp505 1.93 Mg C2' A:5gp505 2.79 Mg C4' A:5gp505 3.63 Mg O2' A:5gp505 1.95 Mg P A:5gp506 4.94 Mg O3P A:5gp506 3.96 Mg O2P A:5gp506 4.53 Mg O A:Hoh508 2.30 Mg O A:Hoh509 2.06 interactive model: Magnesium binding site 2 out of 4 in 1ecb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1ecb. 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: Tyr258, B: Ile301, B: Pro302, B: Asp366, B: Asp367, B: Ser368, B: 5gp505, B: 5gp506, B: Hoh508, B: Hoh509, conact list: Atom Atom Distance (A) Mg CE1 B:Tyr258 4.95 Mg O B:Ile301 4.70 Mg CG2 B:Ile301 4.78 Mg O B:Pro302 4.81 Mg CB B:Asp366 4.68 Mg OD2 B:Asp366 3.66 Mg OD1 B:Asp366 2.33 Mg CG B:Asp366 3.33 Mg CA B:Asp366 4.93 Mg N B:Asp367 4.19 Mg CB B:Asp367 4.49 Mg OD2 B:Asp367 3.72 Mg OD1 B:Asp367 2.16 Mg CG B:Asp367 3.26 Mg CA B:Asp367 4.90 Mg O B:Ser368 4.79 Mg N B:Ser368 4.85 Mg C3' B:5gp505 2.93 Mg C1' B:5gp505 3.86 Mg O4' B:5gp505 4.20 Mg O3' B:5gp505 1.98 Mg C2' B:5gp505 2.86 Mg C4' B:5gp505 3.66 Mg O2' B:5gp505 1.93 Mg P B:5gp506 4.89 Mg O3P B:5gp506 3.89 Mg O2P B:5gp506 4.57 Mg O B:Hoh508 2.08 Mg O B:Hoh509 2.15 interactive model: Magnesium binding site 3 out of 4 in 1ecb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1ecb. 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: C: Tyr258, C: Ile301, C: Pro302, C: Thr304, C: Asp366, C: Asp367, C: Ser368, C: 5gp505, C: 5gp506, C: Hoh508, C: Hoh509, conact list: Atom Atom Distance (A) Mg CE1 C:Tyr258 4.93 Mg O C:Ile301 4.57 Mg CG2 C:Ile301 4.69 Mg O C:Pro302 4.65 Mg OG1 C:Thr304 4.90 Mg CB C:Asp366 4.50 Mg OD2 C:Asp366 3.37 Mg OD1 C:Asp366 2.19 Mg CG C:Asp366 3.12 Mg CA C:Asp366 4.86 Mg N C:Asp367 4.19 Mg CB C:Asp367 4.36 Mg OD2 C:Asp367 2.14 Mg OD1 C:Asp367 3.29 Mg CG C:Asp367 3.02 Mg CA C:Asp367 4.84 Mg O C:Ser368 4.82 Mg N C:Ser368 4.92 Mg C3' C:5gp505 2.83 Mg C1' C:5gp505 3.87 Mg O4' C:5gp505 4.26 Mg O3' C:5gp505 1.82 Mg C2' C:5gp505 2.82 Mg C4' C:5gp505 3.71 Mg O2' C:5gp505 1.95 Mg P C:5gp506 4.77 Mg O3P C:5gp506 4.02 Mg O2P C:5gp506 4.27 Mg O C:Hoh508 2.04 Mg O C:Hoh509 2.06 interactive model: Magnesium binding site 4 out of 4 in 1ecb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1ecb. 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: D: Ile301, D: Pro302, D: Asp366, D: Asp367, D: Ser368, D: 5gp505, D: 5gp506, D: Hoh508, D: Hoh509, conact list: Atom Atom Distance (A) Mg O D:Ile301 4.75 Mg CG2 D:Ile301 4.79 Mg O D:Pro302 4.96 Mg CB D:Asp366 4.53 Mg OD2 D:Asp366 3.33 Mg C D:Asp366 4.94 Mg OD1 D:Asp366 2.20 Mg CG D:Asp366 3.12 Mg CA D:Asp366 4.95 Mg N D:Asp367 4.10 Mg CB D:Asp367 4.25 Mg OD2 D:Asp367 2.65 Mg OD1 D:Asp367 2.57 Mg CG D:Asp367 2.87 Mg CA D:Asp367 4.64 Mg O D:Ser368 4.75 Mg N D:Ser368 4.62 Mg C3' D:5gp505 2.67 Mg C1' D:5gp505 3.82 Mg O4' D:5gp505 4.14 Mg O3' D:5gp505 1.70 Mg C5' D:5gp505 4.95 Mg C2' D:5gp505 2.77 Mg C4' D:5gp505 3.55 Mg O2' D:5gp505 2.02 Mg O3P D:5gp506 4.18 Mg O2P D:5gp506 4.68 Mg O D:Hoh508 2.12 Mg O D:Hoh509 2.27 interactive model: