Calcium in PDB 5sb4: Tubulin-Todalam-8-Complex

The structure of Tubulin-Todalam-8-Complex, PDB code: 5sb4 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)	49.62 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.575, 157.329, 180.728, 90, 90, 90
R / Rfree (%)	19.8 / 23

The structure of Tubulin-Todalam-8-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-8-Complex (pdb code 5sb4). 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-8-Complex, PDB code: 5sb4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Todalam-8-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-8-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:85.0 occ:1.00 O A:GLY44 2.4 88.1 1.0 OE2 A:GLU55 2.4 83.2 1.0 OD1 A:ASP39 2.4 85.6 1.0 OG1 A:THR41 2.5 90.0 1.0 O A:THR41 2.6 91.1 1.0 OE1 A:GLU55 2.8 86.5 1.0 OD2 A:ASP39 2.8 82.8 1.0 CD A:GLU55 2.9 83.3 1.0 CG A:ASP39 2.9 83.8 1.0 CB A:THR41 3.4 88.6 1.0 C A:GLY44 3.5 89.4 1.0 C A:THR41 3.6 92.3 1.0 CA A:THR41 4.0 91.1 1.0 CA A:GLY45 4.1 89.5 1.0 N A:GLY45 4.2 86.7 1.0 CZ A:PHE49 4.2 75.3 1.0 OD1 A:ASN50 4.3 82.3 1.0 N A:THR41 4.3 91.3 1.0 OD2 A:ASP47 4.3 77.7 1.0 CB A:ASP39 4.4 84.4 1.0 CG A:GLU55 4.4 74.4 1.0 N A:GLY44 4.5 91.9 1.0 CA A:GLY44 4.5 89.5 1.0 ND2 A:ASN50 4.6 76.2 1.0 CE2 A:PHE49 4.7 71.7 1.0 CG2 A:THR41 4.7 84.4 1.0 N A:ILE42 4.8 93.9 1.0 CG A:ASN50 4.9 75.3 1.0 NE2 A:HIS61 4.9 81.6 1.0 C A:GLY45 5.0 88.9 1.0

Calcium binding site 2 out of 4 in the Tubulin-Todalam-8-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-8-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:89.8 occ:1.00 O B:HOH616 2.4 65.8 1.0 OE1 B:GLU113 3.0 79.7 1.0 OE2 B:GLU113 3.5 76.8 1.0 CD B:GLU113 3.6 77.3 1.0

Calcium binding site 3 out of 4 in the Tubulin-Todalam-8-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-8-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:66.8 occ:1.00 O C:GLY44 2.4 69.3 1.0 OE2 C:GLU55 2.4 64.2 1.0 O C:THR41 2.4 73.9 1.0 OE1 C:GLU55 2.4 63.9 1.0 O C:HOH609 2.5 61.5 1.0 OG1 C:THR41 2.5 72.0 1.0 OD2 C:ASP39 2.5 60.6 1.0 OD1 C:ASP39 2.6 64.9 1.0 CD C:GLU55 2.8 63.0 1.0 CG C:ASP39 2.9 61.3 1.0 C C:GLY44 3.4 71.2 1.0 C C:THR41 3.4 73.4 1.0 CB C:THR41 3.4 67.8 1.0 CA C:THR41 3.9 69.5 1.0 O C:HOH616 4.1 64.9 1.0 N C:GLY45 4.2 72.3 1.0 CA C:GLY45 4.2 70.4 1.0 N C:THR41 4.2 67.7 1.0 CG C:GLU55 4.3 58.9 1.0 CA C:GLY44 4.4 70.2 1.0 N C:GLY44 4.4 72.8 1.0 OD2 C:ASP47 4.5 69.7 1.0 CB C:ASP39 4.5 61.5 1.0 OD1 C:ASN50 4.5 60.6 1.0 N C:ILE42 4.5 74.7 1.0 NE2 C:HIS61 4.7 56.7 1.0 CZ C:PHE49 4.7 55.7 1.0 CG2 C:THR41 4.8 59.7 1.0 ND2 C:ASN50 4.8 51.5 1.0 CE1 C:PHE49 5.0 55.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Todalam-8-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-8-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:94.1 occ:1.00 O E:HOH316 2.8 68.0 1.0 OD2 E:ASP44 3.3 96.9 1.0 OG A:SER158 4.0 69.4 1.0 O A:GLU196 4.2 68.5 1.0 CG E:ASP44 4.3 97.3 1.0 OD1 E:ASP44 4.6 96.0 1.0 CB A:SER158 4.6 68.7 1.0 OD1 A:ASP199 4.7 68.0 1.0 O A:GLY162 4.7 77.9 1.0 NZ A:LYS166 4.8 68.9 1.0 CA A:HIS197 4.8 60.3 1.0 O A:HIS197 5.0 61.3 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