Calcium in PDB 6fjf: Tubulin-Fcmaytansine Complex

The structure of Tubulin-Fcmaytansine Complex, PDB code: 6fjf 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)	49.55 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.373, 156.739, 180.956, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.8

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

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

The binding sites of Calcium atom in the Tubulin-Fcmaytansine Complex (pdb code 6fjf). 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-Fcmaytansine Complex, PDB code: 6fjf:
Jump to Calcium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Fcmaytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:96.1 occ:1.00 OE2 A:GLU55 2.4 93.5 1.0 OD2 A:ASP39 2.4 72.6 1.0 O A:GLY44 2.4 87.5 1.0 OG1 A:THR41 2.5 92.2 1.0 OD1 A:ASP39 2.6 82.1 1.0 O A:THR41 2.6 99.0 1.0 CG A:ASP39 2.8 74.3 1.0 OE1 A:GLU55 3.0 99.6 1.0 CD A:GLU55 3.0 93.7 1.0 C A:GLY44 3.5 89.8 1.0 CB A:THR41 3.5 96.0 1.0 C A:THR41 3.7 98.5 1.0 OD2 A:ASP47 4.0 82.5 1.0 CA A:THR41 4.0 97.0 1.0 CZ A:PHE49 4.1 61.8 1.0 CA A:GLY45 4.1 0.8 1.0 N A:GLY45 4.2 99.1 1.0 OD1 A:ASN50 4.3 88.2 1.0 CB A:ASP39 4.3 69.6 1.0 N A:THR41 4.4 95.0 1.0 N A:GLY44 4.5 82.6 1.0 CE1 A:PHE49 4.5 66.3 1.0 CA A:GLY44 4.5 84.4 1.0 CG A:GLU55 4.5 84.0 1.0 ND2 A:ASN50 4.6 73.9 1.0 O A:HOH654 4.6 73.9 1.0 NE2 A:HIS61 4.7 80.7 1.0 CG2 A:THR41 4.8 98.5 1.0 N A:ILE42 4.9 97.4 1.0 CG A:ASN50 4.9 75.7 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Fcmaytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:65.4 occ:1.00 OD2 C:ASP39 2.3 55.2 1.0 OE2 C:GLU55 2.4 59.1 1.0 O C:THR41 2.4 58.7 1.0 OG1 C:THR41 2.5 74.8 1.0 OE1 C:GLU55 2.6 59.3 1.0 O C:GLY44 2.6 66.5 1.0 OD1 C:ASP39 2.7 57.9 1.0 CD C:GLU55 2.8 56.9 1.0 CG C:ASP39 2.9 56.9 1.0 C C:GLY44 3.4 69.9 1.0 C C:THR41 3.5 65.7 1.0 CB C:THR41 3.5 67.5 1.0 CA C:THR41 3.9 67.2 1.0 OD2 C:ASP47 3.9 72.7 1.0 N C:GLY45 4.1 71.1 1.0 CA C:GLY45 4.1 74.1 1.0 N C:THR41 4.2 60.8 1.0 CA C:GLY44 4.3 77.9 1.0 CG C:GLU55 4.3 52.7 1.0 CB C:ASP39 4.4 61.3 1.0 OD1 C:ASN50 4.4 48.3 1.0 N C:GLY44 4.4 80.3 1.0 CZ C:PHE49 4.4 43.1 1.0 O C:HOH617 4.5 48.7 1.0 N C:ILE42 4.6 64.1 1.0 O C:HOH714 4.7 56.4 1.0 NE2 C:HIS61 4.7 45.7 1.0 ND2 C:ASN50 4.8 37.0 1.0 CG2 C:THR41 4.8 60.6 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