Magnesium in the structure of Znmg Substituted Aminopeptidase P From E. Coli (pdb 1w7v)

The binding sites of Magnesium atom in the structure of Znmg Substituted Aminopeptidase P From E. Coli (pdb code 1w7v). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1w7v structure was solved by S.C.GRAHAM, C.S.BOND, H.C.FREEMAN, J.M.GUSS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 37.8-2.0 Space group C121 a (A) 111.731 b (A) 236.527 c (A) 137.997 alpha (°) 90.00 beta (°) 106.34 gamma (°) 90.00 Rfactor (%) 15.6 Rfree (%) 18 Magnesium Binding Sites: Magnesium binding site 1 out of 6 in 1w7v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1w7v. 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: Tyr229, A: Asp260, A: Asp271, A: Ile272, A: Thr273, A: Glu383, A: Arg404, A: Glu406, E: Pro1, A: Zn1440, A: Hoh2193, A: Hoh2270, E: Hoh2001, conact list: Atom Atom Distance (A) Mg CE2 A:Tyr229 4.51 Mg CZ A:Tyr229 4.16 Mg CE1 A:Tyr229 4.88 Mg OH A:Tyr229 3.68 Mg CB A:Asp260 4.11 Mg OD2 A:Asp260 2.30 Mg OD1 A:Asp260 2.19 Mg CG A:Asp260 2.57 Mg CA A:Asp260 4.90 Mg O A:Asp271 4.77 Mg CB A:Asp271 4.41 Mg OD2 A:Asp271 3.43 Mg C A:Asp271 4.54 Mg OD1 A:Asp271 1.98 Mg CG A:Asp271 3.05 Mg CA A:Asp271 4.73 Mg O A:Ile272 4.68 Mg N A:Ile272 4.72 Mg C A:Ile272 4.80 Mg CB A:Thr273 4.99 Mg OG1 A:Thr273 3.61 Mg OE1 A:Glu383 3.90 Mg OE2 A:Glu383 4.96 Mg CD A:Glu383 4.79 Mg NE A:Arg404 4.90 Mg OE1 A:Glu406 2.12 Mg CB A:Glu406 4.96 Mg OE2 A:Glu406 3.32 Mg CD A:Glu406 3.05 Mg CG A:Glu406 4.42 Mg N E:Pro1 4.68 Mg CD E:Pro1 4.80 Mg ZN A:Zn1440 3.17 Mg O A:Hoh2193 2.18 Mg O A:Hoh2270 2.09 Mg O E:Hoh2001 3.81 interactive model: Magnesium binding site 2 out of 6 in 1w7v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1w7v. 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: Tyr229, B: Asp260, B: Asp271, B: Ile272, B: Thr273, B: Glu383, B: Arg404, B: Glu406, F: Pro1, B: Zn1440, B: Hoh2230, B: Hoh2344, F: Hoh2001, conact list: Atom Atom Distance (A) Mg CE2 B:Tyr229 4.48 Mg CZ B:Tyr229 4.14 Mg CE1 B:Tyr229 4.87 Mg OH B:Tyr229 3.68 Mg CB B:Asp260 4.06 Mg OD2 B:Asp260 2.22 Mg OD1 B:Asp260 2.18 Mg CG B:Asp260 2.53 Mg CA B:Asp260 4.88 Mg O B:Asp271 4.80 Mg CB B:Asp271 4.38 Mg OD2 B:Asp271 3.35 Mg C B:Asp271 4.54 Mg OD1 B:Asp271 2.00 Mg CG B:Asp271 3.02 Mg CA B:Asp271 4.70 Mg O B:Ile272 4.70 Mg N B:Ile272 4.70 Mg C B:Ile272 4.80 Mg CB B:Thr273 4.98 Mg OG1 B:Thr273 3.61 Mg OE1 B:Glu383 3.99 Mg OE2 B:Glu383 4.92 Mg CD B:Glu383 4.80 Mg NE B:Arg404 4.86 Mg NH2 B:Arg404 4.97 Mg OE1 B:Glu406 2.18 Mg CB B:Glu406 4.98 Mg OE2 B:Glu406 3.33 Mg CD B:Glu406 3.07 Mg CG B:Glu406 4.45 Mg N F:Pro1 4.55 Mg CD F:Pro1 4.85 Mg ZN B:Zn1440 3.19 Mg O B:Hoh2230 2.07 Mg O B:Hoh2344 2.01 Mg O F:Hoh2001 3.81 interactive model: Magnesium binding site 3 out of 6 in 1w7v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1w7v. 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: Glu396, B: Gln397, B: Arg399, B: Hoh2217, B: Hoh2226, B: Hoh2247, B: Hoh2304, B: Hoh2306, B: Hoh2309, B: Hoh2310, B: Hoh2311, conact list: Atom Atom Distance (A) Mg O B:Glu396 4.49 Mg OE2 B:Glu396 3.99 Mg CD B:Glu396 4.95 Mg O B:Gln397 4.21 Mg C B:Gln397 4.77 Mg CA B:Gln397 4.98 Mg O B:Arg399 3.81 Mg O B:Hoh2217 4.94 Mg O B:Hoh2226 3.68 Mg O B:Hoh2247 4.40 Mg O B:Hoh2304 2.11 Mg O B:Hoh2306 2.01 Mg O B:Hoh2309 2.14 Mg O B:Hoh2310 2.14 Mg O B:Hoh2311 4.64 interactive model: Magnesium binding site 4 out of 6 in 1w7v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1w7v. 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: C: Tyr229, C: Asp260, C: Asp271, C: Ile272, C: Thr273, C: Glu383, C: Arg404, C: Glu406, G: Pro1, C: Zn1440, C: Hoh2110, C: Hoh2137, conact list: Atom Atom Distance (A) Mg CE2 C:Tyr229 4.48 Mg CZ C:Tyr229 4.13 Mg CE1 C:Tyr229 4.84 Mg OH C:Tyr229 3.66 Mg CB C:Asp260 4.13 Mg OD2 C:Asp260 2.19 Mg OD1 C:Asp260 2.36 Mg CG C:Asp260 2.60 Mg CA C:Asp260 4.97 Mg O C:Asp271 4.82 Mg CB C:Asp271 4.40 Mg OD2 C:Asp271 3.22 Mg C C:Asp271 4.60 Mg OD1 C:Asp271 2.09 Mg CG C:Asp271 3.00 Mg CA C:Asp271 4.77 Mg O C:Ile272 4.84 Mg N C:Ile272 4.80 Mg C C:Ile272 4.90 Mg OG1 C:Thr273 3.67 Mg OE1 C:Glu383 4.14 Mg OE2 C:Glu383 4.94 Mg CD C:Glu383 4.86 Mg NE C:Arg404 4.88 Mg OE1 C:Glu406 2.23 Mg OE2 C:Glu406 3.36 Mg CD C:Glu406 3.11 Mg CG C:Glu406 4.47 Mg N G:Pro1 4.40 Mg CD G:Pro1 4.70 Mg ZN C:Zn1440 3.10 Mg O C:Hoh2110 2.21 Mg O C:Hoh2137 2.07 interactive model: Magnesium binding site 5 out of 6 in 1w7v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 1w7v. 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: D: Tyr229, D: Asp260, D: Asp271, D: Ile272, D: Thr273, D: Glu383, D: Arg404, D: Glu406, H: Pro1, D: Zn1440, D: Hoh2237, D: Hoh2337, H: Hoh2001, conact list: Atom Atom Distance (A) Mg CE2 D:Tyr229 4.48 Mg CZ D:Tyr229 4.13 Mg CE1 D:Tyr229 4.80 Mg OH D:Tyr229 3.71 Mg CB D:Asp260 4.13 Mg OD2 D:Asp260 2.26 Mg OD1 D:Asp260 2.21 Mg CG D:Asp260 2.58 Mg CA D:Asp260 4.95 Mg O D:Asp271 4.83 Mg CB D:Asp271 4.39 Mg OD2 D:Asp271 3.27 Mg C D:Asp271 4.59 Mg OD1 D:Asp271 2.02 Mg CG D:Asp271 3.00 Mg CA D:Asp271 4.75 Mg O D:Ile272 4.76 Mg N D:Ile272 4.80 Mg C D:Ile272 4.90 Mg OG1 D:Thr273 3.71 Mg OE1 D:Glu383 4.01 Mg OE2 D:Glu383 4.86 Mg CD D:Glu383 4.78 Mg NE D:Arg404 4.85 Mg OE1 D:Glu406 2.20 Mg OE2 D:Glu406 3.36 Mg CD D:Glu406 3.11 Mg CG D:Glu406 4.51 Mg N H:Pro1 4.45 Mg CD H:Pro1 4.69 Mg ZN D:Zn1440 3.14 Mg O D:Hoh2237 2.10 Mg O D:Hoh2337 2.01 Mg O H:Hoh2001 3.78 interactive model: Magnesium binding site 6 out of 6 in 1w7v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 1w7v. 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: D: Glu396, D: Gln397, D: Arg399, D: Hoh2096, D: Hoh2231, D: Hoh2232, D: Hoh2251, D: Hoh2304, D: Hoh2306, D: Hoh2310, D: Hoh2311, D: Hoh2312, conact list: Atom Atom Distance (A) Mg O D:Glu396 4.61 Mg OE2 D:Glu396 4.07 Mg CD D:Glu396 4.97 Mg O D:Gln397 4.26 Mg C D:Gln397 4.78 Mg CA D:Gln397 4.96 Mg O D:Arg399 3.94 Mg O D:Hoh2096 1.98 Mg O D:Hoh2231 4.97 Mg O D:Hoh2232 3.64 Mg O D:Hoh2251 4.50 Mg O D:Hoh2304 2.11 Mg O D:Hoh2306 1.93 Mg O D:Hoh2310 2.14 Mg O D:Hoh2311 2.13 Mg O D:Hoh2312 4.56 interactive model: