Magnesium in the structure of Crystal Structure of A Laci-Family Transcriptional Regulatory Protein From Corynebacterium Glutamicum (pdb 3gyb)

The binding sites of Magnesium atom in the structure of Crystal Structure of A Laci-Family Transcriptional Regulatory Protein From Corynebacterium Glutamicum (pdb code 3gyb). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3gyb structure was solved by K.PALANI, S.K.BURLEY, S.SWAMINATHAN, NEW YORK SGX RESEARCHCENTER FOR STRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 32.5-1.6 Space group P1 a (A) 38.073 b (A) 61.882 c (A) 65.604 alpha (°) 115.83 beta (°) 106.37 gamma (°) 90.50 Rfactor (%) 21.5 Rfree (%) 23.1 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 3gyb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3gyb. 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: Trp77, A: Asp80, A: Asp270, A: Asn271, A: Thr272, A: Asp286, A: Asp287, A: Asn288, A: Ser289, A: Hoh16, A: Hoh356, A: Hoh357, A: Hoh463, A: Hoh464, A: Hoh465, conact list: Atom Atom Distance (A) Mg O A:Trp77 4.30 Mg OD2 A:Asp80 4.05 Mg OD1 A:Asp80 4.05 Mg CG A:Asp80 4.49 Mg O A:Asp270 2.16 Mg CB A:Asp270 4.48 Mg C A:Asp270 3.30 Mg CA A:Asp270 3.98 Mg O A:Asn271 4.04 Mg N A:Asn271 4.36 Mg CB A:Asn271 4.45 Mg C A:Asn271 4.29 Mg CA A:Asn271 4.60 Mg N A:Thr272 4.89 Mg OD1 A:Asp286 4.45 Mg N A:Asp287 4.33 Mg CB A:Asp287 4.42 Mg OD2 A:Asp287 3.45 Mg C A:Asp287 4.85 Mg OD1 A:Asp287 2.12 Mg CG A:Asp287 3.10 Mg CA A:Asp287 4.77 Mg N A:Asn288 4.77 Mg N A:Ser289 3.91 Mg CB A:Ser289 3.17 Mg OG A:Ser289 2.23 Mg CA A:Ser289 4.17 Mg O A:Hoh16 4.73 Mg O A:Hoh356 4.93 Mg O A:Hoh357 4.12 Mg O A:Hoh463 2.17 Mg O A:Hoh464 2.21 Mg O A:Hoh465 2.23 interactive model: Magnesium binding site 2 out of 2 in 3gyb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3gyb. 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: Trp77, B: Asp80, B: Asp270, B: Asn271, B: Thr272, B: Asp286, B: Asp287, B: Asn288, B: Ser289, B: Hoh14, B: Hoh22, B: Hoh36, B: Hoh447, B: Hoh448, B: Hoh449, conact list: Atom Atom Distance (A) Mg O B:Trp77 4.30 Mg OD2 B:Asp80 4.03 Mg OD1 B:Asp80 3.99 Mg CG B:Asp80 4.44 Mg O B:Asp270 2.14 Mg CB B:Asp270 4.45 Mg C B:Asp270 3.29 Mg CA B:Asp270 3.97 Mg O B:Asn271 4.10 Mg N B:Asn271 4.36 Mg CB B:Asn271 4.43 Mg C B:Asn271 4.34 Mg CA B:Asn271 4.61 Mg N B:Thr272 4.95 Mg OD1 B:Asp286 4.43 Mg N B:Asp287 4.30 Mg CB B:Asp287 4.42 Mg OD2 B:Asp287 3.54 Mg C B:Asp287 4.87 Mg OD1 B:Asp287 2.12 Mg CG B:Asp287 3.14 Mg CA B:Asp287 4.76 Mg N B:Asn288 4.81 Mg N B:Ser289 3.95 Mg CB B:Ser289 3.18 Mg OG B:Ser289 2.18 Mg CA B:Ser289 4.19 Mg O B:Hoh14 4.63 Mg O B:Hoh22 4.85 Mg O B:Hoh36 4.12 Mg O B:Hoh447 2.22 Mg O B:Hoh448 2.18 Mg O B:Hoh449 2.19 interactive model: