Magnesium in the structure of Structure of The M1 Alanylaminopeptidase From Malaria Complexed With the Phosphinate Dipeptide Analog (pdb 3ebi)

The binding sites of Magnesium atom in the structure of Structure of The M1 Alanylaminopeptidase From Malaria Complexed With the Phosphinate Dipeptide Analog (pdb code 3ebi). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3ebi structure was solved by S.MCGOWAN, C.J.PORTER, A.M.BUCKLE, J.C.WHISSTOCK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.6-2.0 Space group P212121 a (A) 75.852 b (A) 108.633 c (A) 118.325 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) 22.1 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 3ebi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3ebi. 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: Tyr399, A: Ala434, A: Glu437, A: Asp438, A: Hoh100, A: Hoh103, A: Hoh159, A: Hoh1473, A: Hoh1542, A: Hoh1543, conact list: Atom Atom Distance (A) Mg OH A:Tyr399 4.37 Mg CB A:Ala434 4.20 Mg CA A:Ala434 4.77 Mg OE1 A:Glu437 4.40 Mg OD2 A:Asp438 4.42 Mg OD1 A:Asp438 4.15 Mg CG A:Asp438 4.74 Mg O A:Hoh100 2.51 Mg O A:Hoh103 2.39 Mg O A:Hoh159 3.90 Mg O A:Hoh1473 1.87 Mg O A:Hoh1542 2.19 Mg O A:Hoh1543 2.04 interactive model: Magnesium binding site 2 out of 4 in 3ebi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3ebi. 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: Gly250, A: Leu251, A: Ile295, A: Ile296, A: His297, A: Hoh26, A: Hoh111, A: Hoh1099, A: Hoh1193, A: Hoh1214, A: Hoh1471, A: Hoh1536, conact list: Atom Atom Distance (A) Mg O A:Gly250 2.27 Mg C A:Gly250 3.42 Mg CA A:Gly250 4.06 Mg N A:Leu251 4.52 Mg CA A:Leu251 4.82 Mg O A:Ile295 4.51 Mg CA A:Ile296 4.67 Mg N A:His297 4.92 Mg ND1 A:His297 4.13 Mg CE1 A:His297 4.83 Mg O A:Hoh26 2.15 Mg O A:Hoh111 4.18 Mg O A:Hoh1099 2.35 Mg O A:Hoh1193 4.20 Mg O A:Hoh1214 2.18 Mg O A:Hoh1471 4.40 Mg O A:Hoh1536 2.15 interactive model: Magnesium binding site 3 out of 4 in 3ebi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3ebi. 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: Thr492, A: Glu526, A: Asn527, A: Thr539, A: Ser542, A: His543, A: Hoh112, A: Hoh1177, A: Hoh1224, A: Hoh1430, A: Hoh1537, A: Hoh1538, A: Hoh1539, A: Hoh1540, conact list: Atom Atom Distance (A) Mg CG2 A:Thr492 4.31 Mg OE1 A:Glu526 4.36 Mg OE2 A:Glu526 4.35 Mg CD A:Glu526 4.80 Mg OD1 A:Asn527 4.44 Mg O A:Thr539 4.63 Mg OG A:Ser542 4.31 Mg CB A:His543 4.77 Mg CD2 A:His543 4.73 Mg O A:Hoh112 4.25 Mg O A:Hoh1177 2.17 Mg O A:Hoh1224 4.23 Mg O A:Hoh1430 3.61 Mg O A:Hoh1537 2.20 Mg O A:Hoh1538 2.62 Mg O A:Hoh1539 2.06 Mg O A:Hoh1540 2.18 interactive model: Magnesium binding site 4 out of 4 in 3ebi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3ebi. 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: Lys311, A: Glu957, A: Asn992, A: Asp995, A: Hoh190, A: Hoh1418, A: Hoh1541, conact list: Atom Atom Distance (A) Mg CE A:Lys311 4.96 Mg OE1 A:Glu957 4.94 Mg CB A:Glu957 4.96 Mg OE2 A:Glu957 3.25 Mg CD A:Glu957 3.93 Mg CG A:Glu957 4.08 Mg ND2 A:Asn992 3.98 Mg CG A:Asn992 4.98 Mg OD2 A:Asp995 4.27 Mg O A:Hoh190 4.27 Mg O A:Hoh1418 4.28 Mg O A:Hoh1541 1.98 interactive model: