Magnesium in PDB 6lsm: Tubulin Polymerization Inhibitors

The structure of Tubulin Polymerization Inhibitors, PDB code: 6lsm was solved by L.Gang, Y.X.Wang, J.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.87 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.553, 158.081, 182.23, 90, 90, 90
R / Rfree (%)	18.1 / 22.7

The structure of Tubulin Polymerization Inhibitors also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Tubulin Polymerization Inhibitors (pdb code 6lsm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Tubulin Polymerization Inhibitors, PDB code: 6lsm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin Polymerization Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.3 occ:1.00 O A:HOH604 1.9 53.0 1.0 O A:HOH602 2.0 75.8 1.0 O1B A:GTP501 2.2 42.7 1.0 O1G A:GTP501 2.2 44.0 1.0 PG A:GTP501 3.4 42.8 1.0 PB A:GTP501 3.5 35.2 1.0 OD2 A:ASP69 3.7 57.6 1.0 OE1 A:GLU71 3.7 67.6 1.0 O2G A:GTP501 3.7 43.4 1.0 CG A:GLU71 3.8 57.9 1.0 OD1 A:ASP69 3.9 52.7 1.0 O3B A:GTP501 3.9 50.5 1.0 NZ B:LYS254 4.1 61.7 1.0 CB A:GLN11 4.2 44.1 1.0 CG A:ASP69 4.2 57.0 1.0 CD A:GLU71 4.2 65.3 1.0 N A:GLN11 4.3 40.1 1.0 O3A A:GTP501 4.3 41.3 1.0 CB A:ASP98 4.5 46.1 1.0 OD2 A:ASP98 4.6 55.0 1.0 O2B A:GTP501 4.6 54.9 1.0 O1A A:GTP501 4.7 43.4 1.0 CG A:ASP98 4.7 51.0 1.0 O3G A:GTP501 4.7 37.1 1.0 OE1 A:GLN11 4.8 54.4 1.0 CA A:GLN11 4.8 39.7 1.0

Magnesium binding site 2 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin Polymerization Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:36.5 occ:1.00 O B:HOH615 1.9 59.7 1.0 OE1 B:GLN11 2.0 57.3 1.0 O B:HOH601 2.0 67.2 1.0 O B:HOH620 2.1 55.4 1.0 O B:HOH622 2.1 52.8 1.0 O1A B:GDP501 2.2 40.1 1.0 CD B:GLN11 3.2 56.1 1.0 OD2 B:ASP179 3.3 55.7 1.0 PA B:GDP501 3.7 28.1 1.0 NE2 B:GLN11 4.1 51.5 1.0 OD1 B:ASN101 4.2 41.9 1.0 CB B:GLN11 4.2 40.6 1.0 CG B:GLN11 4.2 47.3 1.0 O3A B:GDP501 4.3 40.8 1.0 CG B:ASP179 4.4 51.9 1.0 C5' B:GDP501 4.5 24.7 1.0 OE1 C:GLU254 4.6 59.7 1.0 O5' B:GDP501 4.6 23.5 1.0 O2A B:GDP501 4.7 28.0 1.0 O1B B:GDP501 4.8 35.9 1.0

Magnesium binding site 3 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin Polymerization Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:87.2 occ:1.00 O B:HOH611 2.1 77.0 1.0 OD2 B:ASP120 4.2 68.6 1.0 OD1 B:ASP120 4.2 67.0 1.0 CB B:ASP116 4.5 41.3 1.0 CG B:ASP120 4.6 67.3 1.0 OD2 B:ASP116 4.7 77.6 1.0 CG B:ASP116 4.9 51.6 1.0

Magnesium binding site 4 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin Polymerization Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:46.6 occ:1.00 O C:HOH601 1.9 59.2 1.0 O1G C:GTP501 1.9 41.4 1.0 O C:HOH606 2.0 51.0 1.0 O1B C:GTP501 2.1 43.6 1.0 O C:HOH614 2.3 42.0 1.0 PG C:GTP501 3.3 34.0 1.0 PB C:GTP501 3.4 31.2 1.0 OE1 C:GLU71 3.5 65.2 1.0 NZ D:LYS254 3.7 50.6 1.0 O3B C:GTP501 3.9 40.8 1.0 O3A C:GTP501 3.9 39.3 1.0 OD2 C:ASP98 4.0 41.4 1.0 O2G C:GTP501 4.0 40.2 1.0 CG C:GLU71 4.1 39.4 1.0 OD2 C:ASP69 4.2 42.8 1.0 OD1 C:ASP69 4.2 40.9 1.0 CD C:GLU71 4.2 58.5 1.0 CB C:ASP98 4.4 31.7 1.0 CB C:GLN11 4.4 32.5 1.0 CG C:ASP98 4.5 34.5 1.0 O3G C:GTP501 4.5 34.2 1.0 CG C:ASP69 4.6 35.9 1.0 O2B C:GTP501 4.7 33.1 1.0 N C:GLN11 4.7 28.7 1.0 OE1 C:GLN11 4.7 50.5 1.0 O1A C:GTP501 4.8 34.2 1.0 CE D:LYS254 4.9 38.7 1.0 PA C:GTP501 5.0 28.2 1.0

Magnesium binding site 5 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin Polymerization Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:65.0 occ:1.00 OE1 D:GLN11 2.4 83.9 1.0 O5' D:GDP600 3.2 67.1 1.0 CD D:GLN11 3.5 87.2 1.0 O3A D:GDP600 3.8 71.3 1.0 OD1 D:ASN101 3.9 70.4 1.0 C5' D:GDP600 4.0 64.9 1.0 NE2 D:GLN11 4.0 78.8 1.0 PA D:GDP600 4.1 58.0 1.0 ND2 D:ASN101 4.4 92.5 1.0 CG D:ASN101 4.5 77.5 1.0 CG D:GLN11 4.7 86.4 1.0 CB D:GLN11 4.7 78.0 1.0 O1A D:GDP600 4.8 59.5 1.0

Magnesium binding site 6 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tubulin Polymerization Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:94.4 occ:1.00 O2B F:ACP402 2.3 127.8 1.0 O1G F:ACP402 3.1 101.5 1.0 OE1 F:GLU331 3.1 100.9 1.0 NZ F:LYS74 3.2 106.1 1.0 OE2 F:GLU331 3.2 108.1 1.0 CD F:GLU331 3.5 95.4 1.0 PB F:ACP402 3.8 124.3 1.0 OD1 F:ASN333 3.8 107.2 1.0 PG F:ACP402 4.3 132.4 1.0 CE F:LYS74 4.4 97.5 1.0 C3B F:ACP402 4.5 112.9 1.0 O1B F:ACP402 4.6 120.8 1.0 O3A F:ACP402 4.8 109.5 1.0 CG F:ASN333 4.9 96.7 1.0 O2G F:ACP402 5.0 105.8 1.0

L.Gang, Y.X.Wang, J.J.Chen. Design, Synthesis, and Bioevaluation of Pyrazolo[1,5-A]Pyrimidine Derivatives As Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site with Potent Anticancer Activities To Be Published.