Magnesium in the structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli (pdb 2o1s)

The binding sites of Magnesium atom in the structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli (pdb code 2o1s). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2o1s structure was solved by S.XIANG, G.USUNOW, G.LANGE, M.BUSCH, L.TONG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.4 Space group P1211 a (A) 86.787 b (A) 171.154 c (A) 94.799 alpha (°) 90.00 beta (°) 107.25 gamma (°) 90.00 Rfactor (%) 19.1 Rfree (%) 23.4 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 2o1s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2o1s. 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: Gly151, A: Asp152, A: Gly153, A: Asn179, A: Asn181, A: Lys284, A: Tdp3001, A: Hoh3100, A: Hoh3108, A: Hoh3137, A: Hoh3138, conact list: Atom Atom Distance (A) Mg C A:Gly151 4.95 Mg CA A:Gly151 4.91 Mg N A:Asp152 4.20 Mg CB A:Asp152 4.52 Mg OD2 A:Asp152 2.29 Mg OD1 A:Asp152 3.48 Mg CG A:Asp152 3.20 Mg CA A:Asp152 4.83 Mg N A:Gly153 4.35 Mg O A:Asn179 4.32 Mg N A:Asn181 4.29 Mg CB A:Asn181 4.36 Mg ND2 A:Asn181 3.33 Mg C A:Asn181 4.80 Mg OD1 A:Asn181 2.17 Mg CG A:Asn181 3.02 Mg CA A:Asn181 4.71 Mg CE A:Lys284 4.34 Mg NZ A:Lys284 4.23 Mg P2 A:Tdp3001 3.12 Mg P1 A:Tdp3001 3.28 Mg O23 A:Tdp3001 2.08 Mg O5G A:Tdp3001 4.21 Mg O22 A:Tdp3001 4.24 Mg O13 A:Tdp3001 4.34 Mg O21 A:Tdp3001 4.26 Mg O11 A:Tdp3001 3.25 Mg O12 A:Tdp3001 2.11 Mg O A:Hoh3100 4.35 Mg O A:Hoh3108 4.24 Mg O A:Hoh3137 2.42 Mg O A:Hoh3138 2.45 interactive model: Magnesium binding site 2 out of 4 in 2o1s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2o1s. 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: Gly151, B: Asp152, B: Gly153, B: Asn179, B: Asn181, B: Dpo4001, B: Hoh4130, conact list: Atom Atom Distance (A) Mg C B:Gly151 4.14 Mg CA B:Gly151 3.77 Mg N B:Asp152 3.58 Mg CB B:Asp152 4.61 Mg OD2 B:Asp152 4.12 Mg OD1 B:Asp152 2.52 Mg CG B:Asp152 3.55 Mg CA B:Asp152 4.61 Mg N B:Gly153 4.65 Mg O B:Asn179 3.34 Mg ND2 B:Asn179 4.31 Mg C B:Asn179 4.56 Mg CG B:Asn179 4.94 Mg N B:Asn181 4.30 Mg CB B:Asn181 4.32 Mg ND2 B:Asn181 3.39 Mg OD1 B:Asn181 2.76 Mg CG B:Asn181 3.20 Mg CA B:Asn181 4.85 Mg O5 B:Dpo4001 4.85 Mg P2 B:Dpo4001 3.38 Mg O2 B:Dpo4001 2.48 Mg P1 B:Dpo4001 3.22 Mg O1 B:Dpo4001 4.68 Mg O7 B:Dpo4001 2.71 Mg O3 B:Dpo4001 3.68 Mg O4 B:Dpo4001 3.13 Mg O6 B:Dpo4001 4.04 Mg O B:Hoh4130 2.53 interactive model: Magnesium binding site 3 out of 4 in 2o1s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2o1s. 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: Asp152, C: Gly153, C: Asn181, C: Glu182, C: Lys284, C: Tdp3002, C: Hoh3121, conact list: Atom Atom Distance (A) Mg N C:Asp152 4.58 Mg CB C:Asp152 4.32 Mg OD2 C:Asp152 2.72 Mg C C:Asp152 4.90 Mg OD1 C:Asp152 2.35 Mg CG C:Asp152 2.86 Mg CA C:Asp152 4.85 Mg N C:Gly153 4.21 Mg CA C:Gly153 4.88 Mg O C:Asn181 4.92 Mg N C:Asn181 4.48 Mg CB C:Asn181 4.70 Mg ND2 C:Asn181 3.92 Mg C C:Asn181 4.63 Mg OD1 C:Asn181 2.32 Mg CG C:Asn181 3.42 Mg CA C:Asn181 4.86 Mg N C:Glu182 4.68 Mg C C:Glu182 4.47 Mg CE C:Lys284 3.84 Mg NZ C:Lys284 3.48 Mg P2 C:Tdp3002 3.59 Mg P1 C:Tdp3002 3.73 Mg O23 C:Tdp3002 2.34 Mg O5G C:Tdp3002 4.29 Mg O22 C:Tdp3002 4.26 Mg O13 C:Tdp3002 4.85 Mg O21 C:Tdp3002 4.89 Mg O11 C:Tdp3002 4.07 Mg O12 C:Tdp3002 2.30 Mg O C:Hoh3121 2.91 interactive model: Magnesium binding site 4 out of 4 in 2o1s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2o1s. 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: Gly151, D: Asp152, D: Gly153, D: Asn179, D: Asp180, D: Asn181, D: Dpo4002, D: Hoh4113, conact list: Atom Atom Distance (A) Mg C D:Gly151 4.79 Mg CA D:Gly151 4.80 Mg N D:Asp152 3.89 Mg CB D:Asp152 4.12 Mg OD2 D:Asp152 2.40 Mg OD1 D:Asp152 2.54 Mg CG D:Asp152 2.72 Mg CA D:Asp152 4.53 Mg N D:Gly153 4.56 Mg O D:Asn179 4.12 Mg C D:Asp180 4.68 Mg O D:Asn181 4.48 Mg N D:Asn181 3.68 Mg CB D:Asn181 2.91 Mg ND2 D:Asn181 4.36 Mg C D:Asn181 4.72 Mg OD1 D:Asn181 3.08 Mg CG D:Asn181 3.25 Mg CA D:Asn181 3.90 Mg O5 D:Dpo4002 5.00 Mg P2 D:Dpo4002 3.94 Mg O2 D:Dpo4002 2.27 Mg P1 D:Dpo4002 3.69 Mg O1 D:Dpo4002 4.79 Mg O7 D:Dpo4002 2.79 Mg O3 D:Dpo4002 4.39 Mg O4 D:Dpo4002 4.03 Mg O D:Hoh4113 2.62 interactive model: