Magnesium in PDB 6lsn: Crystal Structure of Tubulin-Inhibitor Complex

The structure of Crystal Structure of Tubulin-Inhibitor Complex, PDB code: 6lsn was solved by L.Gang, Y.X.Wang, J.J.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.17 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.296, 158.458, 181.959, 90, 90, 90
R / Rfree (%)	17.7 / 22

The structure of Crystal Structure of Tubulin-Inhibitor Complex also contains other interesting chemical elements:

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

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

Magnesium binding site 1 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


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 Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.0 occ:1.00 O1G A:GTP501 2.2 40.9 1.0 O A:HOH619 2.2 32.9 1.0 O A:HOH612 2.2 34.9 1.0 O1B A:GTP501 2.4 32.2 1.0 PG A:GTP501 3.1 43.3 1.0 O2G A:GTP501 3.2 44.7 1.0 PB A:GTP501 3.5 45.2 1.0 O3B A:GTP501 3.6 52.5 1.0 NZ B:LYS254 3.8 45.4 1.0 CG A:GLU71 3.8 72.3 1.0 OD1 A:ASP69 3.9 53.1 1.0 OE1 A:GLU71 3.9 78.2 1.0 OD2 A:ASP69 4.1 55.1 1.0 CB A:ASP98 4.1 38.4 1.0 O3A A:GTP501 4.2 38.1 1.0 CD A:GLU71 4.4 76.8 1.0 OD2 A:ASP98 4.4 62.2 1.0 CG A:ASP69 4.4 54.3 1.0 CG A:ASP98 4.4 49.5 1.0 O3G A:GTP501 4.5 36.9 1.0 CB A:GLN11 4.5 35.2 1.0 N A:GLN11 4.6 38.4 1.0 O2B A:GTP501 4.8 50.5 1.0 OG1 A:THR145 4.8 38.5 1.0 O1A A:GTP501 4.9 40.6 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


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 Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:43.8 occ:1.00 OE1 B:GLN11 2.0 49.3 1.0 O B:HOH646 2.0 48.8 1.0 O B:HOH637 2.1 56.3 1.0 O1A B:GDP501 2.2 41.9 1.0 O B:HOH649 2.2 41.6 1.0 O B:HOH611 2.3 49.8 1.0 CD B:GLN11 3.2 46.4 1.0 PA B:GDP501 3.5 36.8 1.0 OD2 B:ASP179 3.7 55.6 1.0 O3A B:GDP501 4.0 35.6 1.0 CB B:GLN11 4.0 34.6 1.0 CG B:GLN11 4.1 42.1 1.0 NE2 B:GLN11 4.2 45.0 1.0 OD1 B:ASN101 4.3 43.3 1.0 C5' B:GDP501 4.4 35.9 1.0 O5' B:GDP501 4.4 31.1 1.0 O1B B:GDP501 4.5 38.2 1.0 O2A B:GDP501 4.6 34.1 1.0 OE1 C:GLU254 4.6 45.7 1.0 CG B:ASP179 4.7 46.1 1.0 C8 B:GDP501 4.9 40.4 1.0 PB B:GDP501 4.9 43.6 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:72.4 occ:1.00 O B:HOH608 2.2 70.2 1.0 OD2 B:ASP120 4.1 56.4 1.0 OD1 B:ASP120 4.2 61.5 1.0 CB B:ASP116 4.5 42.7 1.0 CG B:ASP120 4.6 60.9 1.0 CG B:ASP116 4.9 56.8 1.0 OD2 B:ASP116 4.9 70.1 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.5 occ:1.00 O1G C:GTP501 2.1 34.0 1.0 O C:HOH622 2.1 30.1 1.0 O C:HOH621 2.1 31.0 1.0 O C:HOH671 2.2 30.2 1.0 O1B C:GTP501 2.4 38.2 1.0 PG C:GTP501 3.3 48.7 1.0 PB C:GTP501 3.5 39.7 1.0 O2G C:GTP501 3.6 37.7 1.0 NZ D:LYS254 3.6 41.9 1.0 OE1 C:GLU71 3.6 64.5 1.0 O3B C:GTP501 3.8 39.5 1.0 OD2 C:ASP98 3.9 49.2 1.0 O3A C:GTP501 4.0 37.8 1.0 CG C:GLU71 4.1 54.6 1.0 OD2 C:ASP69 4.3 37.0 1.0 OD1 C:ASP69 4.3 40.5 1.0 CB C:ASP98 4.3 42.2 1.0 CD C:GLU71 4.3 54.7 1.0 CB C:GLN11 4.4 26.8 1.0 CG C:ASP98 4.5 43.2 1.0 O3G C:GTP501 4.6 33.4 1.0 OE1 C:GLN11 4.7 48.8 1.0 O1A C:GTP501 4.7 36.1 1.0 CG C:ASP69 4.7 38.5 1.0 N C:GLN11 4.7 27.1 1.0 O2B C:GTP501 4.8 41.0 1.0 CE D:LYS254 4.8 34.5 1.0 PA C:GTP501 5.0 43.3 1.0 O D:HOH720 5.0 40.5 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:68.9 occ:1.00 O1A D:GDP600 2.3 77.2 1.0 OE1 D:GLN11 2.4 90.1 1.0 CD D:GLN11 3.4 93.3 1.0 PA D:GDP600 3.5 59.1 1.0 O3A D:GDP600 3.8 56.8 1.0 OD1 D:ASN101 3.8 88.4 1.0 NE2 D:GLN11 3.9 90.1 1.0 C5' D:GDP600 4.0 58.9 1.0 O5' D:GDP600 4.1 64.0 1.0 CB D:GLN11 4.5 86.1 1.0 ND2 D:ASN101 4.6 94.9 1.0 CG D:GLN11 4.6 92.3 1.0 CG D:ASN101 4.6 89.2 1.0 O2A D:GDP600 4.7 56.6 1.0 O1B D:GDP600 4.7 71.3 1.0 PB D:GDP600 4.8 64.6 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:78.3 occ:1.00 O2B F:ACP402 2.5 132.0 1.0 O1G F:ACP402 3.0 147.8 1.0 OE1 F:GLU331 3.1 87.5 1.0 NZ F:LYS74 3.2 86.7 1.0 OE2 F:GLU331 3.3 106.4 1.0 OD1 F:ASN333 3.4 115.7 1.0 CD F:GLU331 3.6 91.6 1.0 PB F:ACP402 3.9 135.9 1.0 CG F:ASN333 4.3 100.2 1.0 PG F:ACP402 4.3 148.4 1.0 C3B F:ACP402 4.5 153.0 1.0 CE F:LYS74 4.5 82.9 1.0 O1B F:ACP402 4.6 133.7 1.0 ND2 F:ASN333 4.6 110.6 1.0 O3A F:ACP402 4.9 121.5 1.0 O2G F:ACP402 5.0 150.7 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.