Magnesium in the structure of Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex (pdb 2vwt)

The binding sites of Magnesium atom in the structure of Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex (pdb code 2vwt). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2vwt structure was solved by D.REA, J.F.RAKUS, J.A.GERLT, V.FULOP, T.D.H.BUGG, D.I.ROPER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 52.7-1.9 Space group C2221 a (A) 105.600 b (A) 137.700 c (A) 124.100 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.8 Rfree (%) 20.6 Magnesium Binding Sites: Magnesium binding site 1 out of 3 in 2vwt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2vwt. 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: Glu48, A: Arg74, A: Gln151, A: Glu153, A: Asp179, B: Val122, A: Pyr302, A: Hoh2039, A: Hoh2040, A: Hoh2067, A: Hoh2154, conact list: Atom Atom Distance (A) Mg OE1 A:Glu48 4.76 Mg NH1 A:Arg74 4.23 Mg NE2 A:Gln151 3.43 Mg OE1 A:Gln151 4.98 Mg CD A:Gln151 4.60 Mg OE1 A:Glu153 2.11 Mg CB A:Glu153 4.67 Mg OE2 A:Glu153 3.52 Mg CD A:Glu153 3.12 Mg CG A:Glu153 4.41 Mg CB A:Asp179 3.94 Mg OD2 A:Asp179 2.23 Mg OD1 A:Asp179 4.26 Mg CG A:Asp179 3.31 Mg O B:Val122 4.90 Mg CG2 B:Val122 4.99 Mg O2 A:Pyr302 2.49 Mg C1 A:Pyr302 3.19 Mg O1 A:Pyr302 4.44 Mg C3 A:Pyr302 4.58 Mg O3 A:Pyr302 2.36 Mg C2 A:Pyr302 3.14 Mg O A:Hoh2039 4.22 Mg O A:Hoh2040 2.27 Mg O A:Hoh2067 4.69 Mg O A:Hoh2154 2.14 interactive model: Magnesium binding site 2 out of 3 in 2vwt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2vwt. 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: Glu48, B: His49, B: Arg74, B: Gln151, B: Glu153, B: Gly176, B: Asp179, C: Val122, B: Pyr302, B: Hoh2035, B: Hoh2038, B: Hoh2061, C: Hoh2094, conact list: Atom Atom Distance (A) Mg OE1 B:Glu48 4.55 Mg NE2 B:His49 4.75 Mg NH1 B:Arg74 4.20 Mg NE2 B:Gln151 3.59 Mg OE1 B:Gln151 4.86 Mg CD B:Gln151 4.60 Mg OE1 B:Glu153 2.18 Mg CB B:Glu153 4.68 Mg OE2 B:Glu153 3.52 Mg CD B:Glu153 3.15 Mg CG B:Glu153 4.46 Mg CA B:Gly176 4.86 Mg N B:Asp179 4.52 Mg CB B:Asp179 3.67 Mg OD2 B:Asp179 2.18 Mg OD1 B:Asp179 4.33 Mg CG B:Asp179 3.26 Mg CA B:Asp179 4.72 Mg O C:Val122 4.32 Mg O2 B:Pyr302 2.21 Mg C1 B:Pyr302 2.95 Mg O1 B:Pyr302 4.21 Mg C3 B:Pyr302 4.39 Mg O3 B:Pyr302 2.21 Mg C2 B:Pyr302 2.94 Mg O B:Hoh2035 2.19 Mg O B:Hoh2038 3.85 Mg O B:Hoh2061 4.56 Mg O C:Hoh2094 2.18 interactive model: Magnesium binding site 3 out of 3 in 2vwt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2vwt. 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: Val122, C: Glu48, C: Arg74, C: Gln151, C: Glu153, C: Asp179, C: Pyr302, A: Hoh2112, C: Hoh2027, C: Hoh2112, C: Hoh2156, conact list: Atom Atom Distance (A) Mg O A:Val122 4.63 Mg OE1 C:Glu48 4.72 Mg NH1 C:Arg74 4.25 Mg NE2 C:Gln151 3.30 Mg OE1 C:Gln151 4.94 Mg CD C:Gln151 4.48 Mg OE1 C:Glu153 2.18 Mg CB C:Glu153 4.61 Mg OE2 C:Glu153 3.27 Mg CD C:Glu153 2.95 Mg CG C:Glu153 4.23 Mg CB C:Asp179 3.80 Mg OD2 C:Asp179 2.26 Mg OD1 C:Asp179 4.31 Mg CG C:Asp179 3.29 Mg O2 C:Pyr302 2.27 Mg C1 C:Pyr302 3.09 Mg O1 C:Pyr302 4.38 Mg C3 C:Pyr302 4.49 Mg O3 C:Pyr302 2.27 Mg C2 C:Pyr302 3.05 Mg O A:Hoh2112 2.26 Mg O C:Hoh2027 4.61 Mg O C:Hoh2112 2.29 Mg O C:Hoh2156 4.50 interactive model: