Calcium in PDB 7z7d: Tubulin-Todalam-Vinblastine-Complex

The structure of Tubulin-Todalam-Vinblastine-Complex, PDB code: 7z7d was solved by T.Muehlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, B.Roy, 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)	45.60 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.286, 157.296, 182.526, 90, 90, 90
R / Rfree (%)	20.4 / 23.6

The structure of Tubulin-Todalam-Vinblastine-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-Vinblastine-Complex (pdb code 7z7d). 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-Vinblastine-Complex, PDB code: 7z7d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Todalam-Vinblastine-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-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:66.5 occ:1.00 O A:HOH658 2.3 49.3 1.0 OD1 A:ASP39 2.3 60.6 1.0 O A:GLY44 2.4 54.8 1.0 OD2 A:ASP39 2.4 66.6 1.0 O A:THR41 2.5 71.3 1.0 OE2 A:GLU55 2.5 69.1 1.0 OG1 A:THR41 2.5 69.2 1.0 CG A:ASP39 2.7 71.5 1.0 OE1 A:GLU55 2.8 74.3 1.0 CD A:GLU55 3.0 70.7 1.0 C A:THR41 3.4 74.9 1.0 CB A:THR41 3.6 61.1 1.0 C A:GLY44 3.6 67.7 1.0 CA A:THR41 3.9 69.0 1.0 N A:THR41 4.0 66.4 1.0 CB A:ASP39 4.2 68.9 1.0 CA A:GLY45 4.4 81.2 1.0 N A:GLY45 4.5 69.5 1.0 N A:GLY44 4.5 67.7 1.0 CG A:GLU55 4.5 78.8 1.0 CZ A:PHE49 4.5 73.9 1.0 OD2 A:ASP47 4.5 75.8 1.0 O A:HOH704 4.6 72.2 1.0 N A:ILE42 4.6 75.4 1.0 CA A:GLY44 4.6 64.5 1.0 OD1 A:ASN50 4.7 58.8 1.0 NE2 A:HIS61 4.7 71.8 1.0 ND2 A:ASN50 4.8 68.6 1.0 CG2 A:THR41 4.9 67.3 1.0 CA A:ASP39 5.0 68.4 1.0 CE1 A:PHE49 5.0 70.4 1.0

Calcium binding site 2 out of 4 in the Tubulin-Todalam-Vinblastine-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-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:93.6 occ:1.00 O B:HOH725 2.4 62.2 1.0 OE1 B:GLU113 3.2 79.2 1.0 OE2 B:GLU113 4.0 74.7 1.0 CD B:GLU113 4.0 75.9 1.0 OE1 B:GLU110 4.8 43.2 1.0

Calcium binding site 3 out of 4 in the Tubulin-Todalam-Vinblastine-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-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:58.1 occ:1.00 OE2 C:GLU55 2.3 54.1 1.0 OG1 C:THR41 2.4 76.4 1.0 OD2 C:ASP39 2.4 52.1 1.0 O C:HOH652 2.4 48.9 1.0 O C:GLY44 2.5 60.4 1.0 O C:THR41 2.5 71.0 1.0 OE1 C:GLU55 2.6 59.5 1.0 OD1 C:ASP39 2.6 50.1 1.0 CD C:GLU55 2.7 62.3 1.0 CG C:ASP39 2.8 56.0 1.0 C C:GLY44 3.5 64.8 1.0 CB C:THR41 3.5 64.3 1.0 C C:THR41 3.5 67.6 1.0 CA C:THR41 3.9 69.1 1.0 CA C:GLY45 4.1 66.4 1.0 N C:GLY45 4.2 63.9 1.0 N C:THR41 4.2 67.6 1.0 CG C:GLU55 4.2 54.0 1.0 CB C:ASP39 4.3 48.6 1.0 CA C:GLY44 4.5 55.4 1.0 O C:HOH702 4.5 57.8 1.0 N C:GLY44 4.5 67.2 1.0 OD2 C:ASP47 4.5 68.2 1.0 OD1 C:ASN50 4.5 54.4 1.0 NE2 C:HIS61 4.6 54.0 1.0 CZ C:PHE49 4.7 55.6 1.0 N C:ILE42 4.7 71.2 1.0 CE1 C:PHE49 4.7 51.3 1.0 CG2 C:THR41 4.7 60.2 1.0 ND2 C:ASN50 4.8 49.5 1.0 O C:HOH758 5.0 61.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Todalam-Vinblastine-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-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:98.2 occ:1.00 O A:HOH701 3.1 58.4 1.0 OD2 E:ASP44 3.4 98.6 1.0 OG A:SER158 3.9 55.7 1.0 NZ A:LYS166 4.1 52.4 1.0 O A:HOH643 4.1 59.8 1.0 O A:GLU196 4.4 57.2 1.0 CB A:SER158 4.4 42.3 1.0 CG E:ASP44 4.5 96.4 1.0 O A:GLY162 4.5 66.3 1.0 O A:HIS197 4.7 44.4 1.0 CA A:HIS197 4.8 45.8 1.0 OD1 A:ASP199 4.8 42.3 1.0 OD1 E:ASP44 4.9 84.5 1.0 C A:HIS197 5.0 51.3 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