Magnesium in PDB 6xes: Tubulin-RB3_SLD in Complex with Compound 40A

The structure of Tubulin-RB3_SLD in Complex with Compound 40A, PDB code: 6xes was solved by S.W.White, M.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.55 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.178, 126.966, 250.155, 90, 90, 90
R / Rfree (%)	17.1 / 22.6

The binding sites of Magnesium atom in the Tubulin-RB3_SLD in Complex with Compound 40A (pdb code 6xes). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Tubulin-RB3_SLD in Complex with Compound 40A, PDB code: 6xes:

Magnesium binding site 1 out of 1 in the Tubulin-RB3_SLD in Complex with Compound 40A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-RB3_SLD in Complex with Compound 40A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:47.2 occ:1.00 O3G C:GTP501 1.9 42.3 1.0 O C:HOH622 2.0 41.8 1.0 O C:HOH620 2.1 39.2 1.0 O C:HOH611 2.2 44.7 1.0 O C:HOH639 2.2 43.9 1.0 O2B C:GTP501 2.3 37.1 1.0 PG C:GTP501 3.1 46.4 1.0 PB C:GTP501 3.3 41.4 1.0 O C:HOH616 3.5 62.3 1.0 O3B C:GTP501 3.6 48.0 1.0 O2G C:GTP501 3.6 47.4 1.0 O3A C:GTP501 3.8 44.8 1.0 OE1 C:GLU71 4.0 72.2 1.0 CB C:GLN11 4.1 35.6 1.0 OD2 C:ASP98 4.3 59.4 1.0 OD1 C:ASP69 4.3 52.0 1.0 O1G C:GTP501 4.3 40.2 1.0 CB C:ASP98 4.4 41.6 1.0 N C:GLN11 4.4 38.5 1.0 OD2 C:ASP69 4.5 55.0 1.0 O1B C:GTP501 4.6 48.7 1.0 O2A C:GTP501 4.6 46.9 1.0 NZ D:LYS252 4.7 65.4 1.0 OE1 C:GLN11 4.7 49.4 1.0 CG C:ASP98 4.7 54.6 1.0 PA C:GTP501 4.8 46.9 1.0 CD C:GLU71 4.8 67.5 1.0 CA C:GLN11 4.8 34.8 1.0 CG C:ASP69 4.8 55.1 1.0

H.Chen, S.Deng, N.Albadari, M.K.Yun, S.Zhang, Y.Li, D.Ma, D.N.Parke, L.Yang, T.N.Seagroves, S.W.White, D.D.Miller, W.Li. Design, Synthesis, and Biological Evaluation of Stable Colchicine-Binding Site Tubulin Inhibitors 6-Aryl-2-Benzoyl-Pyridines As Potential Anticancer Agents. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34378386
DOI: 10.1021/ACS.JMEDCHEM.1C00715