Magnesium in the structure of Linb Complexed With Clindamycin and Ampcpp (pdb 3jz0)

The binding sites of Magnesium atom in the structure of Linb Complexed With Clindamycin and Ampcpp (pdb code 3jz0). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3jz0 structure was solved by M.MORAR, G.D.WRIGHT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.0 Space group P212121 a (A) 63.689 b (A) 96.064 c (A) 102.708 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.9 Rfree (%) 22.1 Magnesium Binding Sites: Magnesium binding site 1 out of 5 in 3jz0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3jz0. 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: Gly28, A: Ser29, A: Asp40, A: Glu42, A: Mg303, A: Apc738, A: Hoh276, A: Hoh322, A: Hoh424, A: Hoh470, conact list: Atom Atom Distance (A) Mg C A:Gly28 4.88 Mg CA A:Gly28 4.46 Mg N A:Ser29 4.21 Mg CB A:Ser29 4.80 Mg OG A:Ser29 4.05 Mg O A:Asp40 3.96 Mg N A:Asp40 4.33 Mg CB A:Asp40 4.40 Mg OD2 A:Asp40 3.51 Mg C A:Asp40 4.36 Mg OD1 A:Asp40 2.02 Mg CG A:Asp40 3.10 Mg CA A:Asp40 4.62 Mg OE1 A:Glu42 2.10 Mg OE2 A:Glu42 3.25 Mg CD A:Glu42 3.01 Mg CG A:Glu42 4.39 Mg MG A:Mg303 3.53 Mg PG A:Apc738 3.33 Mg O3B A:Apc738 3.67 Mg O2G A:Apc738 4.10 Mg PA A:Apc738 3.40 Mg C3A A:Apc738 3.69 Mg O5' A:Apc738 4.14 Mg O2B A:Apc738 2.09 Mg O3G A:Apc738 4.65 Mg O2A A:Apc738 4.65 Mg O1B A:Apc738 4.56 Mg PB A:Apc738 3.21 Mg C5' A:Apc738 3.93 Mg O1G A:Apc738 2.16 Mg O1A A:Apc738 2.22 Mg O A:Hoh276 4.28 Mg O A:Hoh322 2.15 Mg O A:Hoh424 3.94 Mg O A:Hoh470 4.75 interactive model: Magnesium binding site 2 out of 5 in 3jz0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3jz0. 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: Glu42, A: Arg87, A: Glu89, A: Mg300, A: Apc738, A: Cly900, A: Hoh424, A: Hoh470, conact list: Atom Atom Distance (A) Mg CB A:Asp40 4.46 Mg OD2 A:Asp40 2.09 Mg OD1 A:Asp40 3.34 Mg CG A:Asp40 3.07 Mg OE1 A:Glu42 3.64 Mg CB A:Glu42 4.59 Mg OE2 A:Glu42 2.04 Mg CD A:Glu42 3.16 Mg CG A:Glu42 4.41 Mg NH2 A:Arg87 4.57 Mg NH1 A:Arg87 4.46 Mg OE1 A:Glu89 2.05 Mg CB A:Glu89 4.79 Mg OE2 A:Glu89 3.97 Mg CD A:Glu89 3.27 Mg CG A:Glu89 4.32 Mg MG A:Mg300 3.53 Mg PA A:Apc738 3.17 Mg C3A A:Apc738 4.75 Mg O5' A:Apc738 3.89 Mg O2B A:Apc738 4.82 Mg O2A A:Apc738 3.43 Mg C5' A:Apc738 4.13 Mg O1G A:Apc738 4.65 Mg O1A A:Apc738 2.16 Mg C1 A:Cly900 4.18 Mg C2 A:Cly900 3.86 Mg C3 A:Cly900 4.99 Mg O7 A:Cly900 4.90 Mg O4 A:Cly900 3.87 Mg O6 A:Cly900 2.58 Mg O A:Hoh424 4.06 Mg O A:Hoh470 2.02 interactive model: Magnesium binding site 3 out of 5 in 3jz0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3jz0. 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: Asn59, A: Phe62, A: Asp63, A: Hoh351, A: Hoh1031, A: Hoh1032, A: Hoh1033, A: Hoh1034, conact list: Atom Atom Distance (A) Mg O A:Asn59 4.10 Mg C A:Asn59 4.97 Mg CD2 A:Phe62 4.56 Mg N A:Asp63 4.64 Mg CB A:Asp63 4.37 Mg OD2 A:Asp63 3.31 Mg OD1 A:Asp63 2.03 Mg CG A:Asp63 3.01 Mg CA A:Asp63 4.66 Mg O A:Hoh351 4.17 Mg O A:Hoh1031 2.02 Mg O A:Hoh1032 2.17 Mg O A:Hoh1033 1.86 Mg O A:Hoh1034 2.24 interactive model: Magnesium binding site 4 out of 5 in 3jz0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3jz0. 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: Gly28, B: Ser29, B: Asp40, B: Glu42, B: Mg302, B: Apc738, B: Hoh275, B: Hoh297, B: Hoh307, B: Hoh401, conact list: Atom Atom Distance (A) Mg C B:Gly28 4.86 Mg CA B:Gly28 4.48 Mg N B:Ser29 4.14 Mg CB B:Ser29 4.72 Mg OG B:Ser29 4.04 Mg O B:Asp40 4.06 Mg N B:Asp40 4.22 Mg CB B:Asp40 4.43 Mg OD2 B:Asp40 3.59 Mg C B:Asp40 4.41 Mg OD1 B:Asp40 2.11 Mg CG B:Asp40 3.17 Mg CA B:Asp40 4.59 Mg OE1 B:Glu42 2.13 Mg OE2 B:Glu42 3.38 Mg CD B:Glu42 3.09 Mg CG B:Glu42 4.43 Mg MG B:Mg302 3.67 Mg PG B:Apc738 3.21 Mg O3B B:Apc738 3.54 Mg O2G B:Apc738 3.97 Mg PA B:Apc738 3.47 Mg C3A B:Apc738 3.65 Mg O5' B:Apc738 4.15 Mg O2B B:Apc738 2.02 Mg O3G B:Apc738 4.50 Mg O2A B:Apc738 4.77 Mg O1B B:Apc738 4.47 Mg PB B:Apc738 3.12 Mg C5' B:Apc738 3.99 Mg O1G B:Apc738 2.08 Mg O1A B:Apc738 2.33 Mg O B:Hoh275 4.22 Mg O B:Hoh297 3.89 Mg O B:Hoh307 2.12 Mg O B:Hoh401 4.89 interactive model: Magnesium binding site 5 out of 5 in 3jz0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3jz0. 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: Glu42, B: Arg87, B: Glu89, B: Mg301, B: Apc738, B: Cly900, B: Hoh297, B: Hoh401, conact list: Atom Atom Distance (A) Mg CB B:Asp40 4.42 Mg OD2 B:Asp40 2.11 Mg OD1 B:Asp40 3.33 Mg CG B:Asp40 3.06 Mg OE1 B:Glu42 3.63 Mg CB B:Glu42 4.58 Mg OE2 B:Glu42 2.05 Mg CD B:Glu42 3.16 Mg CG B:Glu42 4.42 Mg CZ B:Arg87 4.94 Mg NH2 B:Arg87 4.45 Mg NH1 B:Arg87 4.41 Mg OE1 B:Glu89 1.93 Mg CB B:Glu89 4.76 Mg OE2 B:Glu89 3.80 Mg CD B:Glu89 3.12 Mg CG B:Glu89 4.19 Mg MG B:Mg301 3.67 Mg PA B:Apc738 3.24 Mg C3A B:Apc738 4.79 Mg O5' B:Apc738 4.00 Mg O2B B:Apc738 4.86 Mg O2A B:Apc738 3.53 Mg C5' B:Apc738 4.20 Mg O1G B:Apc738 4.70 Mg O1A B:Apc738 2.19 Mg C1 B:Cly900 4.01 Mg C2 B:Cly900 3.73 Mg C3 B:Cly900 4.86 Mg O7 B:Cly900 4.84 Mg O4 B:Cly900 3.62 Mg O6 B:Cly900 2.49 Mg O B:Hoh297 4.02 Mg O B:Hoh401 2.13 interactive model: