Calcium in PDB 5sb7: Tubulin-Todalam-18-Complex

The structure of Tubulin-Todalam-18-Complex, PDB code: 5sb7 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)	48.08 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.148, 158.288, 179.988, 90, 90, 90
R / Rfree (%)	20.2 / 23.5

The structure of Tubulin-Todalam-18-Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Tubulin-Todalam-18-Complex (pdb code 5sb7). 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-18-Complex, PDB code: 5sb7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:53.8 occ:1.00 O A:GLY44 2.3 53.6 1.0 O A:THR41 2.4 61.1 1.0 OE2 A:GLU55 2.4 53.4 1.0 O A:HOH614 2.5 52.1 1.0 OD2 A:ASP39 2.5 62.4 1.0 OD1 A:ASP39 2.5 60.4 1.0 OG1 A:THR41 2.5 53.1 1.0 OE1 A:GLU55 2.7 56.2 1.0 CG A:ASP39 2.9 63.1 1.0 CD A:GLU55 2.9 62.7 1.0 C A:THR41 3.4 65.0 1.0 CB A:THR41 3.4 56.1 1.0 C A:GLY44 3.5 55.9 1.0 CA A:THR41 3.8 56.9 1.0 N A:THR41 4.2 60.5 1.0 CA A:GLY45 4.2 62.4 1.0 N A:GLY45 4.3 59.4 1.0 N A:GLY44 4.3 60.2 1.0 CB A:ASP39 4.4 58.3 1.0 CG A:GLU55 4.4 58.4 1.0 CZ A:PHE49 4.5 56.0 1.0 CA A:GLY44 4.5 56.5 1.0 OD1 A:ASN50 4.5 53.2 1.0 N A:ILE42 4.6 60.6 1.0 OD2 A:ASP47 4.6 55.8 1.0 NE2 A:HIS61 4.8 62.8 1.0 CG2 A:THR41 4.8 57.6 1.0 ND2 A:ASN50 4.8 49.3 1.0 CE1 A:PHE49 4.9 55.8 1.0

Calcium binding site 2 out of 4 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:88.0 occ:1.00 O B:HOH698 2.4 60.6 1.0 OE1 B:GLU113 2.9 62.3 1.0 OE2 B:GLU113 3.1 66.0 1.0 CD B:GLU113 3.3 65.3 1.0 CG B:GLU113 4.9 50.9 1.0

Calcium binding site 3 out of 4 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:49.3 occ:1.00 O C:GLY44 2.4 43.1 1.0 O C:THR41 2.4 54.8 1.0 O C:HOH643 2.4 40.4 1.0 OD2 C:ASP39 2.5 49.3 1.0 OE2 C:GLU55 2.5 43.1 1.0 OE1 C:GLU55 2.5 45.7 1.0 OG1 C:THR41 2.5 55.9 1.0 OD1 C:ASP39 2.6 48.8 1.0 CD C:GLU55 2.8 48.7 1.0 CG C:ASP39 2.9 47.6 1.0 C C:THR41 3.5 53.7 1.0 C C:GLY44 3.5 51.6 1.0 CB C:THR41 3.6 55.1 1.0 CA C:THR41 4.0 53.5 1.0 O C:HOH614 4.2 45.5 1.0 CA C:GLY45 4.2 55.0 1.0 N C:THR41 4.3 53.7 1.0 N C:GLY45 4.3 55.2 1.0 CG C:GLU55 4.3 44.7 1.0 CB C:ASP39 4.4 48.6 1.0 OD2 C:ASP47 4.4 48.6 1.0 N C:GLY44 4.5 53.6 1.0 OD1 C:ASN50 4.5 48.2 1.0 CA C:GLY44 4.6 50.6 1.0 N C:ILE42 4.6 50.7 1.0 CZ C:PHE49 4.7 45.9 1.0 NE2 C:HIS61 4.7 39.9 1.0 ND2 C:ASN50 4.8 37.1 1.0 CE1 C:PHE49 4.9 41.9 1.0 CG2 C:THR41 4.9 48.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:92.1 occ:1.00 O A:HOH745 2.5 60.2 1.0 O A:HOH722 2.9 54.7 1.0 OD2 E:ASP44 3.3 76.9 1.0 O A:HOH718 3.8 48.9 1.0 O A:GLU196 3.8 55.5 1.0 OG A:SER158 4.3 52.8 1.0 CG E:ASP44 4.3 77.0 1.0 OD1 E:ASP44 4.5 69.5 1.0 CA A:HIS197 4.7 44.7 1.0 OD1 A:ASP199 4.8 49.4 1.0 CB A:SER158 4.9 47.6 1.0 C A:GLU196 4.9 53.4 1.0 NZ A:LYS166 4.9 50.6 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