Calcium in PDB 5sb6: Tubulin-Todalam-10-Complex

The structure of Tubulin-Todalam-10-Complex, PDB code: 5sb6 was solved by T.Muehlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, A.E.Prota, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.47 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.27, 156.726, 180.456, 90, 90, 90
R / Rfree (%)	20.1 / 23.7

The structure of Tubulin-Todalam-10-Complex also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Tubulin-Todalam-10-Complex (pdb code 5sb6). 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-Todalam-10-Complex, PDB code: 5sb6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Todalam-10-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Todalam-10-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:78.5 occ:1.00 O A:GLY44 2.4 84.9 1.0 OE2 A:GLU55 2.4 76.7 1.0 OD1 A:ASP39 2.4 83.2 1.0 OG1 A:THR41 2.5 85.9 1.0 OD2 A:ASP39 2.5 80.3 1.0 O A:THR41 2.5 89.2 1.0 OE1 A:GLU55 2.7 86.5 1.0 CG A:ASP39 2.8 78.1 1.0 CD A:GLU55 2.9 79.7 1.0 CB A:THR41 3.5 83.3 1.0 C A:GLY44 3.5 88.4 1.0 C A:THR41 3.6 91.4 1.0 CA A:THR41 4.0 86.7 1.0 N A:THR41 4.2 88.6 1.0 CA A:GLY45 4.2 87.5 1.0 CZ A:PHE49 4.2 69.1 1.0 CB A:ASP39 4.3 76.8 1.0 N A:GLY45 4.3 87.5 1.0 OD1 A:ASN50 4.4 74.3 1.0 CG A:GLU55 4.4 75.6 1.0 OD2 A:ASP47 4.4 78.7 1.0 N A:GLY44 4.5 87.6 1.0 O A:HOH647 4.6 82.5 1.0 CA A:GLY44 4.6 85.8 1.0 CE1 A:PHE49 4.8 67.3 1.0 ND2 A:ASN50 4.8 68.9 1.0 N A:ILE42 4.8 94.1 1.0 CG2 A:THR41 4.8 83.6 1.0 NE2 A:HIS61 4.9 78.9 1.0

Calcium binding site 2 out of 4 in the Tubulin-Todalam-10-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Todalam-10-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:90.7 occ:1.00 O E:HOH221 2.6 72.1 1.0 O A:HOH653 2.9 61.4 1.0 OD2 E:ASP44 3.6 99.9 1.0 OG A:SER158 4.1 65.3 1.0 O A:HOH603 4.2 61.4 1.0 O A:GLY162 4.4 72.2 1.0 NZ A:LYS166 4.4 60.2 1.0 O A:GLU196 4.5 68.3 1.0 CG E:ASP44 4.6 102.4 1.0 OD1 A:ASP199 4.6 59.8 1.0 CB A:SER158 4.6 62.4 1.0 O A:HIS197 4.8 59.2 1.0 OD1 E:ASP44 4.9 96.8 1.0 CA A:HIS197 5.0 57.8 1.0

Calcium binding site 3 out of 4 in the Tubulin-Todalam-10-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Todalam-10-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:92.0 occ:1.00 OE1 B:GLU113 2.7 88.8 1.0 CD B:GLU113 3.5 87.5 1.0 OE2 B:GLU113 3.5 88.9 1.0 OE1 B:GLU110 4.5 56.8 1.0 CG B:GLU113 5.0 78.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Todalam-10-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Todalam-10-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:65.7 occ:1.00 O C:GLY44 2.3 66.0 1.0 O C:THR41 2.4 69.9 1.0 OG1 C:THR41 2.5 68.6 1.0 O C:HOH608 2.5 58.9 1.0 OD1 C:ASP39 2.5 61.2 1.0 OE1 C:GLU55 2.5 60.8 1.0 OE2 C:GLU55 2.5 64.3 1.0 OD2 C:ASP39 2.5 58.2 1.0 CG C:ASP39 2.8 58.8 1.0 CD C:GLU55 2.8 60.2 1.0 C C:THR41 3.5 70.3 1.0 CB C:THR41 3.5 70.4 1.0 C C:GLY44 3.5 68.0 1.0 CA C:THR41 3.9 66.2 1.0 N C:THR41 4.1 63.7 1.0 O C:HOH629 4.2 57.5 1.0 OD2 C:ASP47 4.3 69.5 1.0 CA C:GLY45 4.3 71.4 1.0 CB C:ASP39 4.3 58.5 1.0 CG C:GLU55 4.4 56.4 1.0 N C:GLY45 4.4 69.9 1.0 OD1 C:ASN50 4.4 57.3 1.0 N C:GLY44 4.5 68.2 1.0 CA C:GLY44 4.5 66.8 1.0 NE2 C:HIS61 4.6 58.1 1.0 N C:ILE42 4.6 70.1 1.0 CZ C:PHE49 4.7 52.8 1.0 CG2 C:THR41 4.8 65.0 1.0 ND2 C:ASN50 4.9 51.9 1.0 CE1 C:PHE49 5.0 54.1 1.0

T.Muhlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, B.Roy, A.E.Prota, A.Cavalli, M.O.Steinmetz. Rational Design of A Novel Tubulin Inhibitor with A Unique Mechanism of Action. Angew.Chem.Int.Ed.Engl. V. 61 04052 2022.
ISSN: ESSN 1521-3773
PubMed: 35404502
DOI: 10.1002/ANIE.202204052