Magnesium in the structure of The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex With Prpp and Magnesium (pdb 1zvw)

The binding sites of Magnesium atom in the structure of The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex With Prpp and Magnesium (pdb code 1zvw). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1zvw structure was solved by C.E.LEE, J.S.LOTT, E.N.BAKER, V.L.ARCUS, F.JAVID-MAJD, C.GOODFELLOW, L.-W.HUNG, TB STRUCTURAL GENOMICS CONSORTIUM(TBSGC), 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) 80.417 b (A) 82.076 c (A) 118.873 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.4 Rfree (%) 25.5 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 1zvw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1zvw. 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: Val106, A: Gly107, A: Ser119, A: Asp251, A: Glu252, A: Mg6001, A: Prp3966, A: Hoh6101, A: Hoh6102, A: Hoh6114, A: Hoh6115, A: Hoh6123, conact list: Atom Atom Distance (A) Mg C A:Val106 4.76 Mg N A:Gly107 3.88 Mg C A:Gly107 4.89 Mg CA A:Gly107 4.02 Mg N A:Ser119 4.46 Mg CB A:Ser119 3.39 Mg OG A:Ser119 2.66 Mg CA A:Ser119 4.48 Mg O A:Asp251 4.35 Mg OD2 A:Asp251 3.61 Mg OD1 A:Asp251 4.48 Mg CG A:Asp251 4.33 Mg OE1 A:Glu252 2.46 Mg OE2 A:Glu252 3.87 Mg CD A:Glu252 3.47 Mg CG A:Glu252 4.70 Mg MG A:Mg6001 3.12 Mg O3B A:Prp3966 2.09 Mg C1 A:Prp3966 4.55 Mg O1 A:Prp3966 4.34 Mg PA A:Prp3966 3.26 Mg O2A A:Prp3966 4.37 Mg O1B A:Prp3966 4.24 Mg PB A:Prp3966 3.31 Mg O2B A:Prp3966 4.39 Mg O4 A:Prp3966 4.23 Mg O3A A:Prp3966 3.46 Mg O1A A:Prp3966 2.16 Mg O A:Hoh6101 2.07 Mg O A:Hoh6102 2.10 Mg O A:Hoh6114 4.20 Mg O A:Hoh6115 3.85 Mg O A:Hoh6123 4.27 interactive model: Magnesium binding site 2 out of 2 in 1zvw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1zvw. 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: Asp111, A: Thr115, A: Asp251, A: Glu252, A: Mg4001, A: Prp3966, A: Hoh6070, A: Hoh6101, A: Hoh6102, A: Hoh6115, A: Hoh6117, A: Hoh6123, conact list: Atom Atom Distance (A) Mg OD2 A:Asp111 4.80 Mg OD1 A:Asp111 4.42 Mg CG A:Asp111 4.85 Mg CB A:Thr115 4.95 Mg OG1 A:Thr115 3.60 Mg O A:Asp251 4.17 Mg N A:Asp251 4.99 Mg CB A:Asp251 4.57 Mg OD2 A:Asp251 3.21 Mg C A:Asp251 4.51 Mg OD1 A:Asp251 2.46 Mg CG A:Asp251 3.20 Mg CA A:Asp251 4.91 Mg OE1 A:Glu252 2.25 Mg CB A:Glu252 4.82 Mg OE2 A:Glu252 4.33 Mg CD A:Glu252 3.15 Mg CG A:Glu252 3.35 Mg MG A:Mg4001 3.12 Mg O3B A:Prp3966 3.65 Mg O1B A:Prp3966 4.86 Mg PB A:Prp3966 4.82 Mg O A:Hoh6070 4.56 Mg O A:Hoh6101 2.47 Mg O A:Hoh6102 4.33 Mg O A:Hoh6115 2.53 Mg O A:Hoh6117 2.14 Mg O A:Hoh6123 2.43 interactive model: