Magnesium in PDB 6xer: Tubulin-RB3_SLD in Complex with Colchicine

The structure of Tubulin-RB3_SLD in Complex with Colchicine, PDB code: 6xer 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)	38.34 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.717, 127.025, 254.208, 90, 90, 90
R / Rfree (%)	16.8 / 22.3

The binding sites of Magnesium atom in the Tubulin-RB3_SLD in Complex with Colchicine (pdb code 6xer). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Tubulin-RB3_SLD in Complex with Colchicine, PDB code: 6xer:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Tubulin-RB3_SLD in Complex with Colchicine


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 Colchicine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:56.0 occ:1.00 O2G A:GTP501 2.0 54.3 1.0 O A:HOH602 2.1 61.2 1.0 O A:HOH601 2.1 60.5 1.0 O A:HOH603 2.2 51.0 1.0 O A:HOH604 2.4 59.2 1.0 O2B A:GTP501 2.4 53.0 1.0 PG A:GTP501 3.3 58.7 1.0 PB A:GTP501 3.5 59.8 1.0 O3B A:GTP501 3.7 56.3 1.0 O3G A:GTP501 3.8 48.3 1.0 OD2 A:ASP98 3.9 84.2 1.0 O3A A:GTP501 3.9 70.3 1.0 OE2 A:GLU71 4.0 103.1 1.0 NZ B:LYS252 4.1 67.7 1.0 CB A:GLN11 4.1 47.7 1.0 OD2 A:ASP69 4.1 66.1 1.0 ND2 B:ASN247 4.3 87.1 1.0 CB A:ASP98 4.4 71.6 1.0 OD1 A:ASP69 4.4 65.6 1.0 OE1 A:GLN11 4.5 63.8 1.0 O1G A:GTP501 4.5 64.4 1.0 CD A:GLU71 4.6 99.4 1.0 CG A:ASP98 4.6 80.1 1.0 N A:GLN11 4.6 47.5 1.0 CG A:ASP69 4.7 66.8 1.0 O2A A:GTP501 4.8 65.2 1.0 O1B A:GTP501 4.9 56.0 1.0 CE B:LYS252 4.9 64.9 1.0 PA A:GTP501 4.9 77.9 1.0 CA A:GLN11 4.9 52.0 1.0 OE1 A:GLU71 5.0 106.3 1.0

Magnesium binding site 2 out of 2 in the Tubulin-RB3_SLD in Complex with Colchicine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-RB3_SLD in Complex with Colchicine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:53.6 occ:1.00 O C:HOH601 2.0 58.8 1.0 O C:HOH603 2.1 60.0 1.0 O C:HOH604 2.1 48.5 1.0 O3G C:GTP501 2.1 43.5 1.0 O C:HOH606 2.2 46.9 1.0 O2B C:GTP501 2.2 51.9 1.0 PG C:GTP501 3.1 55.6 1.0 PB C:GTP501 3.2 59.5 1.0 O3B C:GTP501 3.3 54.2 1.0 O2G C:GTP501 3.7 50.6 1.0 O3A C:GTP501 3.8 60.0 1.0 OD1 C:ASP69 4.0 64.1 1.0 NZ D:LYS252 4.1 57.8 1.0 CB C:GLN11 4.1 57.2 1.0 OE2 C:GLU71 4.1 97.6 1.0 OD2 C:ASP69 4.1 60.2 1.0 N C:GLN11 4.3 49.8 1.0 OD2 C:ASP98 4.4 79.6 1.0 CB C:ASP98 4.4 68.4 1.0 CD C:GLU71 4.4 91.3 1.0 O1G C:GTP501 4.4 55.2 1.0 O1B C:GTP501 4.5 60.2 1.0 OE1 C:GLU71 4.5 97.5 1.0 NE2 C:GLN11 4.5 75.9 1.0 CG C:ASP69 4.5 60.1 1.0 O2A C:GTP501 4.5 56.9 1.0 PA C:GTP501 4.7 63.2 1.0 CA C:GLN11 4.8 55.9 1.0 OG1 C:THR145 4.8 53.2 1.0 CG C:ASP98 4.8 75.0 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