Calcium 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
Magnesium	(Mg)	6 atoms

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

Calcium binding site 1 out of 4 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:79.2 occ:1.00 O A:GLY44 2.4 73.3 1.0 OD1 A:ASP39 2.5 70.5 1.0 OE1 A:GLU55 2.5 86.9 1.0 OD2 A:ASP39 2.5 70.7 1.0 O A:THR41 2.6 92.9 1.0 CG2 A:THR41 2.6 71.6 1.0 OE2 A:GLU55 2.8 84.0 1.0 CG A:ASP39 2.9 66.6 1.0 CD A:GLU55 2.9 80.3 1.0 C A:GLY44 3.5 75.2 1.0 C A:THR41 3.6 87.3 1.0 CB A:THR41 3.7 78.7 1.0 CZ A:PHE49 3.9 69.0 1.0 CA A:GLY45 3.9 78.1 1.0 CA A:THR41 4.0 76.5 1.0 OG1 A:THR41 4.1 87.9 1.0 N A:GLY45 4.1 74.9 1.0 N A:THR41 4.3 73.9 1.0 OD2 A:ASP47 4.3 92.8 1.0 CB A:ASP39 4.4 71.3 1.0 CG A:GLU55 4.4 78.4 1.0 N A:GLY44 4.4 82.1 1.0 OD1 A:ASN50 4.5 75.1 1.0 CA A:GLY44 4.5 76.9 1.0 CE1 A:PHE49 4.6 72.1 1.0 CE1 A:HIS61 4.7 73.8 1.0 N A:ILE42 4.8 82.6 1.0 ND2 A:ASN50 4.8 63.2 1.0 CE2 A:PHE49 4.9 68.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:105.3 occ:1.00 O A:HOH606 2.6 61.7 1.0 O E:HOH213 2.6 69.1 1.0 NZ A:LYS166 3.8 50.0 1.0 OG A:SER158 4.0 52.2 1.0 OD2 E:ASP44 4.1 90.2 1.0 OD1 A:ASP199 4.2 56.4 1.0 O A:LYS164 4.4 75.0 1.0 O A:GLY162 4.4 69.8 1.0 O A:GLU196 4.5 66.7 1.0 O A:HIS197 4.6 58.4 1.0 OD2 A:ASP199 4.6 57.9 1.0 CG A:ASP199 4.8 55.1 1.0 CA A:HIS197 5.0 52.0 1.0 C A:HIS197 5.0 54.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:97.3 occ:1.00 OE2 B:GLU113 2.9 92.7 1.0 CD B:GLU113 3.7 88.4 1.0 OE1 B:GLU113 3.7 97.0 1.0 OE1 B:GLU110 4.5 59.9 1.0 OE2 B:GLU110 4.9 59.7 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:51.6 occ:1.00 O C:HOH612 2.3 50.3 1.0 OD2 C:ASP39 2.4 61.0 1.0 O C:THR41 2.4 79.4 1.0 OE2 C:GLU55 2.4 59.8 1.0 O C:GLY44 2.4 50.2 1.0 OD1 C:ASP39 2.5 54.0 1.0 OE1 C:GLU55 2.7 56.5 1.0 OG1 C:THR41 2.7 68.5 1.0 CG C:ASP39 2.8 58.8 1.0 CD C:GLU55 2.9 54.6 1.0 C C:THR41 3.4 68.6 1.0 C C:GLY44 3.4 56.9 1.0 CB C:THR41 3.5 67.6 1.0 CA C:THR41 3.8 66.2 1.0 N C:GLY45 4.1 54.0 1.0 CA C:GLY45 4.1 59.5 1.0 N C:THR41 4.1 66.2 1.0 CB C:ASP39 4.3 59.6 1.0 CG C:GLU55 4.4 51.7 1.0 N C:GLY44 4.4 54.5 1.0 CA C:GLY44 4.5 54.6 1.0 OD2 C:ASP47 4.5 70.5 1.0 N C:ILE42 4.6 68.7 1.0 NE2 C:HIS61 4.7 43.9 1.0 CZ C:PHE49 4.7 48.3 1.0 OD1 C:ASN50 4.7 57.4 1.0 CG2 C:THR41 4.9 61.4 1.0 CE1 C:PHE49 4.9 57.3 1.0 ND2 C:ASN50 5.0 48.3 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.