Calcium in PDB 5s5f: Tubulin-Z87615031-Complex

The structure of Tubulin-Z87615031-Complex, PDB code: 5s5f was solved by T.Muehlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.43 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.828, 158.374, 179.214, 90, 90, 90
R / Rfree (%)	23.6 / 26.2

The structure of Tubulin-Z87615031-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z87615031-Complex (pdb code 5s5f). 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-Z87615031-Complex, PDB code: 5s5f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z87615031-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z87615031-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:77.0 occ:1.00 O A:GLY44 2.4 77.1 1.0 OG1 A:THR41 2.4 81.7 1.0 OE2 A:GLU55 2.4 74.0 1.0 OD1 A:ASP39 2.5 82.1 1.0 OD2 A:ASP39 2.6 75.0 1.0 O A:THR41 2.6 85.7 1.0 CG A:ASP39 2.9 76.6 1.0 OE1 A:GLU55 2.9 76.1 1.0 CD A:GLU55 3.0 75.0 1.0 C A:GLY44 3.4 78.8 1.0 CB A:THR41 3.5 82.7 1.0 C A:THR41 3.6 85.2 1.0 CA A:GLY45 4.0 80.3 1.0 CA A:THR41 4.0 88.7 1.0 N A:GLY45 4.0 75.0 1.0 OD2 A:ASP47 4.1 76.6 1.0 CZ A:PHE49 4.2 69.0 1.0 OD1 A:ASN50 4.2 75.3 1.0 N A:THR41 4.3 88.5 1.0 CB A:ASP39 4.4 76.3 1.0 N A:GLY44 4.4 80.3 1.0 CA A:GLY44 4.4 79.8 1.0 CG A:GLU55 4.5 70.5 1.0 ND2 A:ASN50 4.6 66.4 1.0 CE1 A:PHE49 4.7 64.4 1.0 CG2 A:THR41 4.8 75.3 1.0 NE2 A:HIS61 4.8 74.7 1.0 N A:ILE42 4.9 86.5 1.0 C A:GLY45 4.9 82.4 1.0 CG A:ASN50 4.9 66.7 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z87615031-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z87615031-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:77.2 occ:1.00 O E:HOH201 2.5 61.5 1.0 O A:HOH672 3.1 50.1 1.0 O A:HOH649 3.2 40.1 1.0 OG A:SER158 3.8 46.8 1.0 OD2 E:ASP44 3.9 71.8 1.0 CB A:SER158 4.0 46.7 1.0 NZ A:LYS166 4.0 38.5 1.0 O A:GLY162 4.2 63.9 1.0 CA A:SER158 4.6 47.0 1.0 O A:HOH675 4.7 56.4 1.0 O A:GLU196 4.8 49.2 1.0 O A:HIS197 4.8 41.7 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z87615031-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z87615031-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:78.2 occ:1.00 OE1 B:GLU113 2.6 58.2 1.0 CD B:GLU113 3.5 55.2 1.0 OE2 B:GLU113 3.6 53.5 1.0 OE1 B:GLU110 4.3 37.5 1.0 CG B:GLU113 4.9 47.1 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z87615031-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z87615031-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:48.8 occ:1.00 O C:THR41 2.4 53.2 1.0 O C:GLY44 2.4 51.0 1.0 OE1 C:GLU55 2.4 45.5 1.0 OE2 C:GLU55 2.4 43.9 1.0 OD2 C:ASP39 2.5 43.9 1.0 O C:HOH606 2.5 43.0 1.0 OG1 C:THR41 2.5 52.5 1.0 OD1 C:ASP39 2.6 48.1 1.0 CD C:GLU55 2.8 45.9 1.0 CG C:ASP39 2.9 46.4 1.0 C C:THR41 3.4 56.5 1.0 CB C:THR41 3.5 55.4 1.0 C C:GLY44 3.6 51.6 1.0 CA C:THR41 3.9 52.9 1.0 N C:THR41 4.2 49.6 1.0 CG C:GLU55 4.3 43.2 1.0 OD2 C:ASP47 4.3 53.8 1.0 CA C:GLY45 4.3 56.9 1.0 CB C:ASP39 4.4 43.5 1.0 N C:GLY45 4.4 57.3 1.0 N C:GLY44 4.5 53.5 1.0 OD1 C:ASN50 4.6 46.0 1.0 N C:ILE42 4.6 53.2 1.0 CZ C:PHE49 4.6 39.5 1.0 NE2 C:HIS61 4.6 37.1 1.0 CA C:GLY44 4.7 50.0 1.0 O C:HOH775 4.8 45.5 1.0 CG2 C:THR41 4.8 48.2 1.0 ND2 C:ASN50 4.8 40.7 1.0 CE1 C:PHE49 4.9 39.0 1.0

T.Muhlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz. Comprehensive Analysis of Binding Sites in Tubulin. Angew.Chem.Int.Ed.Engl. V. 60 13331 2021.
ISSN: ESSN 1521-3773
PubMed: 33951246
DOI: 10.1002/ANIE.202100273