Magnesium in PDB 6jcj: Structure of Crolibulin in Complex with Tubulin

The structure of Structure of Crolibulin in Complex with Tubulin, PDB code: 6jcj was solved by Z.Zhang, J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.42 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.544, 157.329, 184.031, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 28.2

The structure of Structure of Crolibulin in Complex with Tubulin also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Magnesium atom in the Structure of Crolibulin in Complex with Tubulin (pdb code 6jcj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Crolibulin in Complex with Tubulin, PDB code: 6jcj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Crolibulin in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Crolibulin in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:23.4 occ:1.00 O A:HOH608 2.0 13.1 1.0 O1G A:GTP501 2.0 19.7 1.0 O A:HOH604 2.0 8.6 1.0 O A:HOH611 2.0 31.7 1.0 O1B A:GTP501 2.1 18.9 1.0 O A:HOH610 2.1 17.7 1.0 PB A:GTP501 3.2 19.2 1.0 PG A:GTP501 3.2 20.2 1.0 O3B A:GTP501 3.4 21.6 1.0 O2G A:GTP501 3.8 20.2 1.0 O3A A:GTP501 3.8 20.2 1.0 OD1 A:ASP69 4.0 27.8 1.0 OE2 A:GLU71 4.0 35.9 1.0 OD2 A:ASP69 4.2 27.0 1.0 CB A:GLN11 4.2 24.0 1.0 CG A:GLU71 4.3 37.0 1.0 OD2 A:ASP98 4.4 30.2 1.0 O3G A:GTP501 4.5 18.5 1.0 O2B A:GTP501 4.5 20.7 1.0 N A:GLN11 4.5 26.4 1.0 CG A:ASP69 4.5 28.6 1.0 CB A:ASP98 4.6 35.3 1.0 O1A A:GTP501 4.6 19.9 1.0 CD A:GLU71 4.7 36.0 1.0 CG A:ASP98 4.7 32.9 1.0 PA A:GTP501 4.8 19.8 1.0 OE1 A:GLN11 4.8 27.1 1.0 CA A:GLN11 4.9 23.8 1.0

Magnesium binding site 2 out of 3 in the Structure of Crolibulin in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Crolibulin in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:59.8 occ:1.00 OE1 B:GLN11 2.4 39.6 1.0 OD2 B:ASP177 2.5 69.7 1.0 O1A B:GDP501 2.7 15.5 1.0 CD B:GLN11 3.5 37.0 1.0 O B:HOH611 3.5 21.6 1.0 CG B:ASP177 3.7 55.4 1.0 PA B:GDP501 4.0 13.7 1.0 NE2 B:GLN11 4.1 36.7 1.0 OE2 C:GLU254 4.3 46.7 1.0 OD1 B:ASP177 4.3 51.9 1.0 C5' B:GDP501 4.4 14.5 1.0 O3A B:GDP501 4.5 13.7 1.0 O5' B:GDP501 4.6 13.7 1.0 CG B:GLN11 4.6 32.4 1.0 OD1 B:ASN99 4.7 19.7 1.0 CB B:GLN11 4.7 28.5 1.0 CB B:ASP177 4.8 51.7 1.0 C8 B:GDP501 4.9 16.6 1.0

Magnesium binding site 3 out of 3 in the Structure of Crolibulin in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Crolibulin in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:16.5 occ:1.00 O1G C:GTP501 1.9 13.1 1.0 O C:HOH617 1.9 16.1 1.0 O C:HOH625 1.9 10.5 1.0 O C:HOH633 2.1 10.1 1.0 O C:HOH607 2.1 16.1 1.0 O1B C:GTP501 2.2 15.5 1.0 PG C:GTP501 3.2 13.6 1.0 PB C:GTP501 3.3 15.8 1.0 O3B C:GTP501 3.6 14.4 1.0 O2G C:GTP501 3.6 13.8 1.0 O3A C:GTP501 3.8 14.6 1.0 OE2 C:GLU71 4.1 32.8 1.0 OD1 C:ASP69 4.2 20.5 1.0 OD2 C:ASP98 4.3 21.0 1.0 CB C:GLN11 4.3 19.5 1.0 OD2 C:ASP69 4.4 21.6 1.0 CG C:GLU71 4.4 31.1 1.0 O3G C:GTP501 4.4 12.2 1.0 CB C:ASP98 4.4 23.3 1.0 OE1 C:GLN11 4.6 21.1 1.0 N C:GLN11 4.6 19.0 1.0 O1A C:GTP501 4.6 16.0 1.0 CG C:ASP98 4.7 22.4 1.0 O2B C:GTP501 4.7 16.3 1.0 CG C:ASP69 4.7 20.8 1.0 CD C:GLU71 4.8 33.3 1.0 PA C:GTP501 4.8 14.9 1.0

Z.Zhang, C.Wang, L.Ma, X.Jiang, C.Wu, Y.Wang, Y.Jiang, W.Zheng, Y.Yang, Y.Ma, J.Yang. Molecular Mechanism of Crolibulin in Complex with Tubulin Provides A Rationale For Drug Design. Biochem. Biophys. Res. V. 511 381 2019COMMUN..
ISSN: ESSN 1090-2104
PubMed: 30803758
DOI: 10.1016/J.BBRC.2019.02.064