Calcium in PDB 6fii: Tubulin-Spongistatin Complex

The structure of Tubulin-Spongistatin Complex, PDB code: 6fii was solved by G.Menchon, A.E.Prota, D.Lucena Angell, P.Bucher, R.Mueller, I.Paterson, J.F.Diaz, K.-H.Altmann, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.17 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.670, 159.920, 181.010, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 21.6

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

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	1 atom

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

Calcium binding site 1 out of 3 in the Tubulin-Spongistatin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Spongistatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:93.4 occ:1.00 O A:GLY44 2.3 85.7 1.0 OE2 A:GLU55 2.4 85.2 1.0 OD1 A:ASP39 2.4 83.2 1.0 O A:THR41 2.5 0.4 1.0 OD2 A:ASP39 2.5 86.0 1.0 OG1 A:THR41 2.7 82.9 1.0 CG A:ASP39 2.8 89.5 1.0 OE1 A:GLU55 3.0 91.2 1.0 CD A:GLU55 3.1 88.2 1.0 CB A:THR41 3.5 90.7 1.0 C A:THR41 3.5 0.8 1.0 C A:GLY44 3.5 96.6 1.0 CA A:THR41 3.9 96.0 1.0 N A:THR41 4.1 95.5 1.0 OD1 A:ASP47 4.2 99.5 1.0 CA A:GLY45 4.2 0.6 1.0 CB A:ASP39 4.3 94.2 1.0 CZ A:PHE49 4.3 78.3 1.0 N A:GLY45 4.3 0.8 1.0 N A:GLY44 4.5 0.8 1.0 CG A:GLU55 4.6 86.2 1.0 CA A:GLY44 4.6 99.6 1.0 OD1 A:ASN50 4.6 79.9 1.0 N A:ILE42 4.7 0.3 1.0 NE2 A:HIS61 4.8 89.2 1.0 CG2 A:THR41 4.9 89.4 1.0 ND2 A:ASN50 4.9 73.1 1.0 CE2 A:PHE49 5.0 74.4 1.0

Calcium binding site 2 out of 3 in the Tubulin-Spongistatin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Spongistatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:0.3 occ:1.00 OE1 B:GLU113 2.7 97.8 1.0 CD B:GLU113 3.5 92.3 1.0 OE2 B:GLU113 3.5 0.9 1.0 OE1 B:GLU110 4.7 64.5 1.0 CG B:GLU113 4.9 70.6 1.0

Calcium binding site 3 out of 3 in the Tubulin-Spongistatin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Spongistatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:69.5 occ:1.00 O C:THR41 2.4 74.8 1.0 O C:GLY44 2.4 76.4 1.0 OD2 C:ASP39 2.5 62.2 1.0 OG1 C:THR41 2.5 70.6 1.0 OE1 C:GLU55 2.5 49.9 1.0 OD1 C:ASP39 2.6 60.8 1.0 O C:HOH602 2.6 68.4 1.0 OE2 C:GLU55 2.6 54.3 1.0 CG C:ASP39 2.9 65.7 1.0 CD C:GLU55 2.9 52.3 1.0 C C:THR41 3.4 75.2 1.0 CB C:THR41 3.5 71.6 1.0 C C:GLY44 3.6 81.1 1.0 CA C:THR41 3.8 72.9 1.0 N C:THR41 4.2 70.4 1.0 O C:HOH635 4.2 54.6 1.0 CA C:GLY45 4.4 82.9 1.0 CB C:ASP39 4.4 69.5 1.0 OD2 C:ASP47 4.4 83.3 1.0 N C:GLY45 4.4 83.8 1.0 CG C:GLU55 4.5 50.1 1.0 N C:ILE42 4.5 74.3 1.0 N C:GLY44 4.6 84.8 1.0 CA C:GLY44 4.6 81.9 1.0 CZ C:PHE49 4.7 46.6 1.0 OD1 C:ASN50 4.7 47.0 1.0 NE2 C:HIS61 4.8 54.5 1.0 CG2 C:THR41 4.8 66.4 1.0 CE1 C:PHE49 4.9 43.6 1.0 CA C:ILE42 5.0 69.0 1.0

G.Menchon, A.E.Prota, D.Lucena-Agell, P.Bucher, R.Jansen, H.Irschik, R.Muller, I.Paterson, J.F.Diaz, K.H.Altmann, M.O.Steinmetz. A Fluorescence Anisotropy Assay to Discover and Characterize Ligands Targeting the Maytansine Site of Tubulin. Nat Commun V. 9 2106 2018.
ISSN: ESSN 2041-1723
PubMed: 29844393
DOI: 10.1038/S41467-018-04535-8