Calcium in PDB 5s5y: Tubulin-Z26781952-Complex

The structure of Tubulin-Z26781952-Complex, PDB code: 5s5y 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)	63.31 / 2.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.96, 158.75, 179.65, 90, 90, 90
R / Rfree (%)	20.2 / 23.1

The structure of Tubulin-Z26781952-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z26781952-Complex (pdb code 5s5y). 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-Z26781952-Complex, PDB code: 5s5y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z26781952-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z26781952-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:84.9 occ:1.00 O A:GLY44 2.2 87.3 1.0 OD2 A:ASP39 2.3 83.8 1.0 OE2 A:GLU55 2.4 83.8 1.0 O A:HOH612 2.5 84.0 1.0 OD1 A:ASP39 2.5 91.1 1.0 O A:THR41 2.6 95.4 1.0 OG1 A:THR41 2.6 86.6 1.0 OE1 A:GLU55 2.6 86.4 1.0 CG A:ASP39 2.8 87.1 1.0 CD A:GLU55 2.8 83.1 1.0 C A:GLY44 3.3 89.9 1.0 CB A:THR41 3.6 95.2 1.0 C A:THR41 3.6 95.7 1.0 CA A:THR41 4.0 97.4 1.0 CA A:GLY45 4.1 95.6 1.0 N A:GLY45 4.1 92.9 1.0 N A:GLY44 4.2 91.3 1.0 CB A:ASP39 4.3 87.5 1.0 N A:THR41 4.3 95.9 1.0 CG A:GLU55 4.3 79.5 1.0 CA A:GLY44 4.4 92.1 1.0 CZ A:PHE49 4.4 77.4 1.0 OD1 A:ASN50 4.5 87.9 1.0 OD2 A:ASP47 4.6 87.0 1.0 NE2 A:HIS61 4.6 83.0 1.0 ND2 A:ASN50 4.7 78.5 1.0 N A:ILE42 4.8 92.3 1.0 CE1 A:PHE49 4.8 77.4 1.0 CG2 A:THR41 4.9 83.0 1.0 C A:GLY45 5.0 97.8 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z26781952-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z26781952-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:99.6 occ:1.00 O A:HOH639 3.4 61.9 1.0 OD2 E:ASP44 3.6 109.0 1.0 OG A:SER158 3.6 66.1 1.0 NZ A:LYS166 4.1 60.3 1.0 CB A:SER158 4.1 71.0 1.0 O A:GLY162 4.3 90.4 1.0 O A:GLU196 4.5 73.1 1.0 CA A:SER158 4.7 71.1 1.0 CG E:ASP44 4.7 105.9 1.0 O A:HIS197 4.8 63.7 1.0 CA A:HIS197 4.9 69.2 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z26781952-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z26781952-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:107.5 occ:1.00 OE1 B:GLU113 2.5 76.0 1.0 CD B:GLU113 3.4 73.0 1.0 OE2 B:GLU113 3.5 78.7 1.0 OE1 B:GLU110 4.4 53.2 1.0 CG B:GLU113 4.8 69.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z26781952-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z26781952-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca604 b:72.9 occ:1.00 O C:GLY44 2.3 78.4 1.0 OE2 C:GLU55 2.4 66.6 1.0 OD2 C:ASP39 2.4 70.5 1.0 O C:THR41 2.4 76.3 1.0 OE1 C:GLU55 2.5 72.8 1.0 OD1 C:ASP39 2.5 72.2 1.0 O C:HOH702 2.6 67.8 1.0 OG1 C:THR41 2.6 78.9 1.0 CD C:GLU55 2.8 70.4 1.0 CG C:ASP39 2.8 72.2 1.0 C C:THR41 3.4 81.1 1.0 C C:GLY44 3.5 79.1 1.0 CB C:THR41 3.5 79.2 1.0 CA C:THR41 3.9 81.9 1.0 N C:THR41 4.2 81.4 1.0 CG C:GLU55 4.3 66.7 1.0 CB C:ASP39 4.3 74.6 1.0 CA C:GLY45 4.3 79.5 1.0 N C:GLY45 4.3 82.3 1.0 N C:GLY44 4.4 81.5 1.0 OD2 C:ASP47 4.5 75.0 1.0 CA C:GLY44 4.5 81.0 1.0 N C:ILE42 4.6 80.0 1.0 OD1 C:ASN50 4.6 68.9 1.0 NE2 C:HIS61 4.7 63.6 1.0 CZ C:PHE49 4.7 63.2 1.0 CG2 C:THR41 4.9 69.0 1.0 ND2 C:ASN50 4.9 60.1 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