Magnesium in the structure of BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2 (pdb 1e42)

The binding sites of Magnesium atom in the structure of BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2 (pdb code 1e42). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1e42 structure was solved by D.J.OWEN, P.R.EVANS, H.T.MCMAHON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 67.4-1.7 Space group C121 a (A) 97.040 b (A) 124.590 c (A) 67.640 alpha (°) 90.00 beta (°) 124.18 gamma (°) 90.00 Rfactor (%) 19.6 Rfree (%) 24.6 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1e42 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1e42. 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: Glu828, A: Gln869, A: Asn872, A: Tyr874, A: Hoh2032, A: Hoh2198, A: Hoh2201, A: Hoh2332, A: Hoh2337, A: Hoh2338, A: Hoh2340, conact list: Atom Atom Distance (A) Mg CB A:Glu828 4.89 Mg CG A:Glu828 4.69 Mg CA A:Glu828 4.89 Mg O A:Gln869 4.38 Mg N A:Asn872 4.65 Mg CB A:Asn872 4.43 Mg ND2 A:Asn872 3.62 Mg OD1 A:Asn872 2.06 Mg CG A:Asn872 3.14 Mg CA A:Asn872 4.65 Mg OH A:Tyr874 4.10 Mg O A:Hoh2032 3.90 Mg O A:Hoh2198 2.07 Mg O A:Hoh2201 3.32 Mg O A:Hoh2332 2.08 Mg O A:Hoh2337 2.07 Mg O A:Hoh2338 2.07 Mg O A:Hoh2340 2.09 interactive model: Magnesium binding site 2 out of 4 in 1e42 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1e42. 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: Glu828, B: Gln869, B: Asn872, B: Tyr874, B: Hoh2032, B: Hoh2225, B: Hoh2351, B: Hoh2355, B: Hoh2357, B: Hoh2358, B: Hoh2361, conact list: Atom Atom Distance (A) Mg CG B:Glu828 4.90 Mg O B:Gln869 4.28 Mg OE1 B:Gln869 4.80 Mg N B:Asn872 4.62 Mg CB B:Asn872 4.41 Mg ND2 B:Asn872 3.68 Mg OD1 B:Asn872 2.07 Mg CG B:Asn872 3.16 Mg CA B:Asn872 4.61 Mg CZ B:Tyr874 4.99 Mg OH B:Tyr874 3.92 Mg O B:Hoh2032 4.22 Mg O B:Hoh2225 2.07 Mg O B:Hoh2351 2.09 Mg O B:Hoh2355 4.32 Mg O B:Hoh2357 2.06 Mg O B:Hoh2358 2.08 Mg O B:Hoh2361 2.08 interactive model: Magnesium binding site 3 out of 4 in 1e42 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1e42. 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: Trp841, B: Glu849, B: Gln851, B: Glu902, B: Ser915, B: Hoh2253, B: Hoh2330, B: Hoh2331, B: Hoh2332, B: Hoh2334, B: Hoh2389, B: Hoh2390, conact list: Atom Atom Distance (A) Mg CZ2 B:Trp841 4.96 Mg OE1 B:Glu849 3.32 Mg OE2 B:Glu849 2.15 Mg CD B:Glu849 3.09 Mg CG B:Glu849 4.48 Mg NE2 B:Gln851 4.08 Mg OE1 B:Glu902 4.21 Mg CD B:Glu902 5.00 Mg CB B:Ser915 4.61 Mg OG B:Ser915 4.23 Mg O B:Hoh2253 2.08 Mg O B:Hoh2330 2.08 Mg O B:Hoh2331 2.08 Mg O B:Hoh2332 2.07 Mg O B:Hoh2334 4.47 Mg O B:Hoh2389 2.04 Mg O B:Hoh2390 4.59 interactive model: Magnesium binding site 4 out of 4 in 1e42 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1e42. 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: Lys842, B: Asp843, B: Ile844, B: Asn846, B: Hoh2199, B: Hoh2315, B: Hoh2316, B: Hoh2317, B: Hoh2321, B: Hoh2325, B: Hoh2327, conact list: Atom Atom Distance (A) Mg O B:Lys842 2.08 Mg CB B:Lys842 4.26 Mg C B:Lys842 3.21 Mg CA B:Lys842 3.85 Mg O B:Asp843 4.60 Mg N B:Asp843 4.32 Mg C B:Asp843 4.69 Mg CA B:Asp843 4.61 Mg O B:Ile844 4.44 Mg ND2 B:Asn846 4.88 Mg OD1 B:Asn846 4.20 Mg CG B:Asn846 4.84 Mg O B:Hoh2199 2.07 Mg O B:Hoh2315 2.08 Mg O B:Hoh2316 2.08 Mg O B:Hoh2317 2.07 Mg O B:Hoh2321 4.90 Mg O B:Hoh2325 2.06 Mg O B:Hoh2327 3.94 interactive model: