Magnesium in the structure of Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains (pdb 2fq1)

The binding sites of Magnesium atom in the structure of Crystal Structure of the Two-Domain Non-Ribosomal Peptide Synthetase Entb Containing Isochorismate Lyase and Aryl-Carrier Protein Domains (pdb code 2fq1). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2fq1 structure was solved by E.J.DRAKE, D.A.NICOLAI, A.M.GULICK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.3 Space group P212121 a (A) 50.889 b (A) 82.331 c (A) 164.730 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 24.1 Magnesium Binding Sites: Magnesium binding site 1 out of 8 in 2fq1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2fq1. 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: His154, A: Glu185, B: Lys191, B: Tyr192, B: Arg196, A: Hoh1112, A: Hoh1113, A: Hoh1114, B: Hoh1055, B: Hoh1056, B: Hoh1057, conact list: Atom Atom Distance (A) Mg NE2 A:His154 3.77 Mg CD2 A:His154 3.92 Mg CE1 A:His154 4.73 Mg CG A:His154 4.97 Mg OE1 A:Glu185 4.92 Mg OE2 A:Glu185 2.82 Mg CD A:Glu185 3.75 Mg CG A:Glu185 3.86 Mg O B:Lys191 4.61 Mg C B:Lys191 4.78 Mg CG B:Lys191 4.16 Mg N B:Tyr192 4.81 Mg CD2 B:Tyr192 4.77 Mg CA B:Tyr192 4.71 Mg CZ B:Arg196 4.25 Mg NE B:Arg196 4.21 Mg NH2 B:Arg196 3.78 Mg O A:Hoh1112 3.55 Mg O A:Hoh1113 4.94 Mg O A:Hoh1114 4.73 Mg O B:Hoh1055 2.26 Mg O B:Hoh1056 2.74 Mg O B:Hoh1057 4.70 interactive model: Magnesium binding site 2 out of 8 in 2fq1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2fq1. 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: Asp40, A: Lys107, A: Val108, A: Asp110, A: Hoh1004, conact list: Atom Atom Distance (A) Mg OD1 A:Asp40 4.15 Mg CB A:Lys107 4.82 Mg O A:Val108 4.87 Mg N A:Asp110 4.76 Mg CB A:Asp110 4.72 Mg OD2 A:Asp110 3.90 Mg OD1 A:Asp110 2.33 Mg CG A:Asp110 3.45 Mg CA A:Asp110 4.85 Mg O A:Hoh1004 4.69 interactive model: Magnesium binding site 3 out of 8 in 2fq1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2fq1. 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: Asp234, A: Asp274, A: Hoh1016, conact list: Atom Atom Distance (A) Mg CB A:Asp234 4.61 Mg OD1 A:Asp234 4.29 Mg CG A:Asp234 4.97 Mg OD2 A:Asp274 3.90 Mg OD1 A:Asp274 3.74 Mg CG A:Asp274 4.25 Mg O A:Hoh1016 2.86 interactive model: Magnesium binding site 4 out of 8 in 2fq1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2fq1. 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: Asp227, A: Gly242, A: Leu243, A: Asp244, A: Arg247, A: Hoh1043, A: Hoh1056, A: Hoh1067, A: Hoh1087, conact list: Atom Atom Distance (A) Mg OD2 A:Asp227 3.00 Mg OD1 A:Asp227 4.34 Mg CG A:Asp227 4.02 Mg O A:Gly242 2.71 Mg C A:Gly242 3.82 Mg CA A:Gly242 4.40 Mg N A:Leu243 4.88 Mg C A:Leu243 4.61 Mg N A:Asp244 4.18 Mg CB A:Asp244 4.34 Mg OD2 A:Asp244 3.38 Mg OD1 A:Asp244 2.49 Mg CG A:Asp244 3.15 Mg CA A:Asp244 4.45 Mg CZ A:Arg247 4.98 Mg NH2 A:Arg247 4.60 Mg NH1 A:Arg247 4.50 Mg O A:Hoh1043 4.79 Mg O A:Hoh1056 2.53 Mg O A:Hoh1067 3.09 Mg O A:Hoh1087 4.77 interactive model: Magnesium binding site 5 out of 8 in 2fq1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 2fq1. 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: Lys68, A: Gln69, A: His70, A: Asn71, A: Hoh1014, A: Hoh1057, A: Hoh1058, A: Hoh1111, conact list: Atom Atom Distance (A) Mg O A:Lys68 4.92 Mg O A:Gln69 2.45 Mg CB A:Gln69 4.72 Mg C A:Gln69 3.53 Mg CG A:Gln69 4.17 Mg CA A:Gln69 4.06 Mg N A:His70 4.66 Mg ND2 A:Asn71 4.90 Mg OD1 A:Asn71 4.93 Mg O A:Hoh1014 4.00 Mg O A:Hoh1057 2.03 Mg O A:Hoh1058 2.99 Mg O A:Hoh1111 2.49 interactive model: Magnesium binding site 6 out of 8 in 2fq1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 2fq1. 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: Lys68, B: Gln69, B: His70, B: Asn71, B: Hoh1043, conact list: Atom Atom Distance (A) Mg O B:Lys68 4.63 Mg O B:Gln69 2.49 Mg CB B:Gln69 4.75 Mg C B:Gln69 3.52 Mg CG B:Gln69 4.33 Mg CA B:Gln69 3.98 Mg N B:His70 4.67 Mg ND2 B:Asn71 4.90 Mg O B:Hoh1043 2.26 interactive model: Magnesium binding site 7 out of 8 in 2fq1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 2fq1. 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: Asp40, B: Lys107, B: Val108, B: Asp110, B: Hoh1025, B: Hoh1030, B: Hoh1047, B: Hoh1052, B: Hoh1076, B: Hoh1100, conact list: Atom Atom Distance (A) Mg OD1 B:Asp40 4.24 Mg CB B:Lys107 4.98 Mg CD B:Lys107 4.72 Mg O B:Val108 4.92 Mg N B:Asp110 4.88 Mg CB B:Asp110 4.68 Mg OD2 B:Asp110 3.72 Mg OD1 B:Asp110 2.27 Mg CG B:Asp110 3.35 Mg CA B:Asp110 4.89 Mg O B:Hoh1025 4.90 Mg O B:Hoh1030 4.61 Mg O B:Hoh1047 2.65 Mg O B:Hoh1052 2.07 Mg O B:Hoh1076 4.28 Mg O B:Hoh1100 2.34 interactive model: Magnesium binding site 8 out of 8 in 2fq1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 2fq1. 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: Glu13, B: His15, B: Asp16, B: Hoh1008, B: Hoh1024, B: Hoh1102, B: Hoh1103, conact list: Atom Atom Distance (A) Mg OE2 B:Glu13 4.39 Mg NE2 B:His15 3.31 Mg CD2 B:His15 4.37 Mg CE1 B:His15 4.10 Mg OD2 B:Asp16 4.95 Mg OD1 B:Asp16 4.71 Mg O B:Hoh1008 2.20 Mg O B:Hoh1024 4.49 Mg O B:Hoh1102 3.22 Mg O B:Hoh1103 2.49 interactive model: