Magnesium in the structure of The Crystal Structure of A Minus-End Directed Microtubule Motor Protein Ncd Reveals Variable Dimer Conformations (pdb 1cz7)

The binding sites of Magnesium atom in the structure of The Crystal Structure of A Minus-End Directed Microtubule Motor Protein Ncd Reveals Variable Dimer Conformations (pdb code 1cz7). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1cz7 structure was solved by F.K.KOZIELSKI, S.DE BONIS, W.BURMEISTER, C.COHEN-ADDAD, R.WADE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-2.9 Space group C2221 a (A) 116.194 b (A) 148.827 c (A) 261.516 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 25.8 Rfree (%) 29.4 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1cz7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1cz7. 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: Thr441, A: Asp580, A: Adp800, conact list: Atom Atom Distance (A) Mg N A:Thr441 4.32 Mg CB A:Thr441 3.41 Mg CG2 A:Thr441 4.33 Mg OG1 A:Thr441 2.10 Mg CA A:Thr441 4.40 Mg OD2 A:Asp580 4.74 Mg OD1 A:Asp580 4.61 Mg O3B A:Adp800 2.75 Mg PA A:Adp800 4.22 Mg O2A A:Adp800 4.41 Mg O1B A:Adp800 3.39 Mg PB A:Adp800 3.28 Mg O5' A:Adp800 4.69 Mg O2B A:Adp800 4.71 Mg O3A A:Adp800 2.96 interactive model: Magnesium binding site 2 out of 4 in 1cz7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1cz7. 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: Lys440, B: Thr441, B: Ser551, B: Asp580, B: Leu581, B: Adp801, conact list: Atom Atom Distance (A) Mg CB B:Lys440 4.83 Mg CE B:Lys440 4.87 Mg N B:Thr441 4.34 Mg CB B:Thr441 3.93 Mg CG2 B:Thr441 4.91 Mg OG1 B:Thr441 2.57 Mg CA B:Thr441 4.69 Mg CA B:Ser551 4.97 Mg OD1 B:Asp580 4.49 Mg O B:Leu581 4.86 Mg O3B B:Adp801 2.65 Mg O1B B:Adp801 3.55 Mg PB B:Adp801 3.51 Mg O2B B:Adp801 4.92 Mg O3A B:Adp801 3.66 interactive model: Magnesium binding site 3 out of 4 in 1cz7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1cz7. 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: Lys440, C: Thr441, C: Asp580, C: Adp802, C: Hoh37, conact list: Atom Atom Distance (A) Mg CB C:Lys440 4.96 Mg N C:Thr441 4.31 Mg CB C:Thr441 3.65 Mg CG2 C:Thr441 4.70 Mg OG1 C:Thr441 2.45 Mg CA C:Thr441 4.51 Mg OD2 C:Asp580 4.31 Mg OD1 C:Asp580 4.10 Mg CG C:Asp580 4.62 Mg O3B C:Adp802 2.43 Mg PA C:Adp802 4.47 Mg O2A C:Adp802 4.56 Mg O1B C:Adp802 3.45 Mg PB C:Adp802 3.22 Mg O2B C:Adp802 4.62 Mg O3A C:Adp802 3.13 Mg O C:Hoh37 2.38 interactive model: Magnesium binding site 4 out of 4 in 1cz7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1cz7. 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: Lys440, D: Thr441, D: Asp580, D: Adp803, D: Hoh152, conact list: Atom Atom Distance (A) Mg CB D:Lys440 4.99 Mg CE D:Lys440 4.65 Mg N D:Thr441 4.45 Mg CB D:Thr441 3.84 Mg CG2 D:Thr441 4.84 Mg OG1 D:Thr441 2.47 Mg CA D:Thr441 4.70 Mg OD2 D:Asp580 4.38 Mg OD1 D:Asp580 4.22 Mg CG D:Asp580 4.77 Mg O3B D:Adp803 2.26 Mg PA D:Adp803 4.55 Mg O2A D:Adp803 4.69 Mg O1B D:Adp803 3.28 Mg PB D:Adp803 3.09 Mg O2B D:Adp803 4.49 Mg O3A D:Adp803 3.14 Mg O D:Hoh152 4.17 interactive model: