Calcium in PDB 8c0f: Tubulin-PTC596 Complex

The structure of Tubulin-PTC596 Complex, PDB code: 8c0f was solved by A.E.Prota, T.Muehlethaler, M.Weetall, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.55 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.68, 158.26, 180.54, 90, 90, 90
R / Rfree (%)	19.4 / 22.5

The structure of Tubulin-PTC596 Complex also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Fluorine	(F)	5 atoms

The binding sites of Calcium atom in the Tubulin-PTC596 Complex (pdb code 8c0f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tubulin-PTC596 Complex, PDB code: 8c0f:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-PTC596 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:80.6 occ:1.00 O A:GLY44 2.3 83.2 1.0 OD2 A:ASP39 2.4 80.8 1.0 OE2 A:GLU55 2.4 68.3 1.0 O A:THR41 2.4 97.8 1.0 OD1 A:ASP39 2.5 83.8 1.0 OG1 A:THR41 2.7 76.0 1.0 OE1 A:GLU55 2.7 81.9 1.0 CG A:ASP39 2.8 84.4 1.0 CD A:GLU55 2.9 78.7 1.0 C A:THR41 3.5 93.6 1.0 C A:GLY44 3.5 90.3 1.0 CB A:THR41 3.6 81.5 1.0 CA A:THR41 3.9 90.2 1.0 OD2 A:ASP47 4.1 95.4 1.0 CA A:GLY45 4.2 93.1 1.0 N A:THR41 4.2 91.6 1.0 CZ A:PHE49 4.2 79.2 1.0 CB A:ASP39 4.3 82.1 1.0 N A:GLY45 4.3 93.8 1.0 CG A:GLU55 4.4 74.2 1.0 N A:GLY44 4.4 88.8 1.0 OD1 A:ASN50 4.5 79.0 1.0 O A:HOH670 4.6 71.1 1.0 CE1 A:PHE49 4.6 77.9 1.0 CA A:GLY44 4.6 89.8 1.0 N A:ILE42 4.7 99.5 1.0 NE2 A:HIS61 4.7 77.4 1.0 ND2 A:ASN50 4.8 68.6 1.0 CG2 A:THR41 5.0 81.5 1.0

Calcium binding site 2 out of 2 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-PTC596 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:64.7 occ:1.00 O C:THR41 2.3 72.6 1.0 OE1 C:GLU55 2.4 55.2 1.0 O C:GLY44 2.4 69.0 1.0 OE2 C:GLU55 2.5 63.9 1.0 OD2 C:ASP39 2.5 55.6 1.0 OG1 C:THR41 2.5 71.2 1.0 OD1 C:ASP39 2.5 60.1 1.0 O C:HOH614 2.6 48.5 1.0 CD C:GLU55 2.8 58.1 1.0 CG C:ASP39 2.9 56.6 1.0 C C:THR41 3.3 73.3 1.0 CB C:THR41 3.4 72.9 1.0 C C:GLY44 3.6 79.3 1.0 CA C:THR41 3.8 69.9 1.0 N C:THR41 4.1 69.6 1.0 O C:HOH612 4.2 60.8 1.0 CG C:GLU55 4.3 52.1 1.0 CA C:GLY45 4.3 75.5 1.0 CB C:ASP39 4.4 58.3 1.0 N C:GLY45 4.4 80.5 1.0 N C:GLY44 4.5 84.6 1.0 N C:ILE42 4.5 70.4 1.0 OD2 C:ASP47 4.5 71.4 1.0 OD1 C:ASN50 4.6 50.1 1.0 CA C:GLY44 4.6 79.2 1.0 CZ C:PHE49 4.7 61.6 1.0 NE2 C:HIS61 4.7 49.2 1.0 CG2 C:THR41 4.8 64.4 1.0 CE1 C:PHE49 4.9 61.0 1.0 O C:HOH725 4.9 60.3 1.0 CA C:ILE42 5.0 65.9 1.0 ND2 C:ASN50 5.0 44.5 1.0

F.Jernigan, A.Branstrom, J.D.Baird, L.Cao, M.Dali, B.Furia, M.J.Kim, K.O'keefe, R.Kong, O.L.Laskin, J.M.Colacino, M.Pykett, A.Mollin, J.Sheedy, M.Dumble, Y.-C.Moon, R.Sheridan, T.Muehlethaler, R.J.Spiegel, A.E.Prota, M.O.Steinmetz, M.Weetall. Preclinical and Early Clinical Development of PTC596, A Novel Small-Molecule Tubulin-Binding Agent Mol Cancer Ther V. 20 1846 2021.
ISSN: ISSN 1535-7163
PubMed: 34315764
DOI: 10.1158/1535-7163.MCT-20-0774