Calcium 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:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	1 atom

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

Calcium binding site 1 out of 4 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin Polymerization Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:80.5 occ:1.00 OD1 A:ASP39 2.4 54.4 1.0 O A:GLY44 2.4 67.4 1.0 O A:THR41 2.5 81.2 1.0 OD2 A:ASP39 2.6 74.4 1.0 OE1 A:GLU55 2.7 74.0 1.0 OE2 A:GLU55 2.8 80.4 1.0 CG A:ASP39 2.8 71.8 1.0 CG2 A:THR41 3.0 72.4 1.0 CD A:GLU55 3.1 78.3 1.0 C A:GLY44 3.5 80.3 1.0 C A:THR41 3.6 85.9 1.0 CB A:THR41 3.9 59.9 1.0 CA A:GLY45 4.0 81.4 1.0 CA A:THR41 4.1 76.5 1.0 N A:GLY45 4.1 58.2 1.0 OG1 A:THR41 4.2 80.0 1.0 CZ A:PHE49 4.2 78.0 1.0 N A:THR41 4.2 59.2 1.0 OD2 A:ASP47 4.4 86.4 1.0 CB A:ASP39 4.4 77.3 1.0 N A:GLY44 4.5 88.5 1.0 OD1 A:ASN50 4.5 72.7 1.0 CA A:GLY44 4.6 83.3 1.0 CG A:GLU55 4.6 73.2 1.0 NE2 A:HIS61 4.7 79.8 1.0 N A:ILE42 4.7 82.1 1.0 CE1 A:PHE49 4.9 70.9 1.0

Calcium binding site 2 out of 4 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin Polymerization Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:113.8 occ:1.00 O E:HOH202 2.1 73.3 1.0 NZ A:LYS166 3.8 48.2 1.0 OG A:SER158 3.9 52.6 1.0 OD2 E:ASP44 4.0 96.8 1.0 OD1 A:ASP199 4.1 53.0 1.0 OD2 A:ASP199 4.4 48.5 1.0 O A:LYS164 4.4 79.3 1.0 O A:GLY162 4.5 63.2 1.0 O A:GLU196 4.5 65.7 1.0 O A:HIS197 4.7 55.6 1.0 CG A:ASP199 4.7 57.2 1.0 CA A:HIS197 4.9 54.6 1.0 C A:HIS197 4.9 54.9 1.0 CB A:SER158 5.0 51.8 1.0

Calcium binding site 3 out of 4 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin Polymerization Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:104.0 occ:1.00 OE1 B:GLU113 3.0 93.5 1.0 OE2 B:GLU113 3.1 108.2 1.0 CD B:GLU113 3.5 102.2 1.0 OE1 B:GLU110 4.4 56.3 1.0 OE2 B:GLU110 4.8 68.2 1.0 CG B:GLU113 5.0 56.7 1.0

Calcium binding site 4 out of 4 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin Polymerization Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:57.8 occ:1.00 OE2 C:GLU55 2.3 61.3 1.0 OD2 C:ASP39 2.3 48.1 1.0 O C:THR41 2.4 71.2 1.0 OD1 C:ASP39 2.5 59.4 1.0 O C:GLY44 2.6 59.9 1.0 OG1 C:THR41 2.6 79.6 1.0 CG C:ASP39 2.8 51.2 1.0 OE1 C:GLU55 2.8 65.1 1.0 CD C:GLU55 2.9 55.4 1.0 C C:THR41 3.4 63.0 1.0 CB C:THR41 3.5 67.2 1.0 C C:GLY44 3.5 57.3 1.0 CA C:THR41 3.9 66.2 1.0 CA C:GLY45 4.0 57.7 1.0 N C:THR41 4.1 55.7 1.0 N C:GLY45 4.2 58.3 1.0 CB C:ASP39 4.3 50.2 1.0 OD2 C:ASP47 4.4 72.8 1.0 CG C:GLU55 4.4 55.3 1.0 N C:GLY44 4.5 60.8 1.0 CA C:GLY44 4.5 66.1 1.0 OD1 C:ASN50 4.5 57.3 1.0 O C:HOH602 4.5 58.5 1.0 N C:ILE42 4.6 63.4 1.0 CZ C:PHE49 4.7 52.2 1.0 NE2 C:HIS61 4.7 44.6 1.0 CG2 C:THR41 4.9 61.7 1.0 ND2 C:ASN50 4.9 50.6 1.0 CE1 C:PHE49 4.9 59.8 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.