Magnesium in PDB 3cjo: Crystal Structure of Ksp in Complex with Inhibitor 30

The structure of Crystal Structure of Ksp in Complex with Inhibitor 30, PDB code: 3cjo was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.758, 79.374, 158.853, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 26.1

The structure of Crystal Structure of Ksp in Complex with Inhibitor 30 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of Ksp in Complex with Inhibitor 30 (pdb code 3cjo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Ksp in Complex with Inhibitor 30, PDB code: 3cjo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ksp in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Ksp in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:23.4 occ:1.00 OG1 A:THR112 2.1 16.5 1.0 O3B A:ADP601 2.1 27.8 1.0 PB A:ADP601 3.3 27.1 1.0 CB A:THR112 3.4 19.0 1.0 O1B A:ADP601 3.6 27.5 1.0 N A:THR112 4.0 22.8 1.0 O A:HOH761 4.0 29.5 1.0 OD2 A:ASP265 4.0 24.1 1.0 O A:SER232 4.0 32.9 1.0 OD1 A:ASP265 4.1 22.8 1.0 O A:HOH716 4.2 21.0 1.0 CA A:THR112 4.2 21.3 1.0 O2B A:ADP601 4.3 29.0 1.0 CG2 A:THR112 4.3 14.4 1.0 O A:HOH717 4.3 29.8 1.0 O3A A:ADP601 4.4 28.5 1.0 O2A A:ADP601 4.4 34.0 1.0 O A:HOH730 4.4 24.9 1.0 CG A:ASP265 4.5 22.6 1.0 CE A:LYS111 4.6 17.8 1.0 CB A:LYS111 4.7 19.9 1.0 O A:HOH708 4.7 10.6 1.0 C A:SER232 4.9 31.9 1.0 PA A:ADP601 4.9 32.4 1.0 NZ A:LYS111 4.9 22.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ksp in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Ksp in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:30.1 occ:1.00 OG1 B:THR112 1.9 23.7 1.0 O3B B:ADP600 2.4 26.2 1.0 CB B:THR112 3.3 22.4 1.0 PB B:ADP600 3.5 25.9 1.0 O1B B:ADP600 3.5 26.6 1.0 O B:HOH733 3.8 25.6 1.0 OD2 B:ASP265 3.9 39.6 1.0 OD1 B:ASP265 3.9 38.0 1.0 O B:SER232 4.0 33.1 1.0 N B:THR112 4.0 25.3 1.0 O B:HOH750 4.1 36.2 1.0 CA B:THR112 4.2 25.4 1.0 CG2 B:THR112 4.2 17.1 1.0 O B:HOH715 4.3 36.2 1.0 CG B:ASP265 4.4 34.9 1.0 O2B B:ADP600 4.5 27.5 1.0 O3A B:ADP600 4.5 27.5 1.0 O2A B:ADP600 4.6 35.6 1.0 O B:HOH710 4.6 16.7 1.0 O B:HOH708 4.6 5.9 1.0 CE B:LYS111 4.8 20.9 1.0 PA B:ADP600 4.9 33.9 1.0 C B:SER232 4.9 31.6 1.0 O1A B:ADP600 4.9 31.6 1.0 NZ B:LYS111 5.0 24.7 1.0 CB B:LYS111 5.0 25.8 1.0

C.D.Cox, P.J.Coleman, M.J.Breslin, D.B.Whitman, R.M.Garbaccio, M.E.Fraley, C.A.Buser, E.S.Walsh, K.Hamilton, M.D.Schaber, R.B.Lobell, W.Tao, J.P.Davide, R.E.Diehl, M.T.Abrams, V.J.South, H.E.Huber, M.Torrent, T.Prueksaritanont, C.Li, D.E.Slaughter, E.Mahan, C.Fernandez-Metzler, Y.Yan, L.C.Kuo, N.E.Kohl, G.D.Hartman. Kinesin Spindle Protein (Ksp) Inhibitors. 9. Discovery of (2S)-4-(2,5-Difluorophenyl)-N-[(3R,4S)-3-Fluoro-1- Methylpiperidin-4-Yl]-2-(Hydroxymethyl)-N-Methyl-2- Phenyl-2,5-Dihydro-1H-Pyrrole-1-Carboxamide (Mk-0731) For the Treatment of Taxane-Refractory Cancer. J.Med.Chem. V. 51 4239 2008.
ISSN: ISSN 0022-2623
PubMed: 18578472
DOI: 10.1021/JM800386Y