Calcium in PDB 5s4l: Tubulin-Z1891773393-Complex

The structure of Tubulin-Z1891773393-Complex, PDB code: 5s4l 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)	63.66 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.37, 159.78, 178.97, 90, 90, 90
R / Rfree (%)	20.2 / 23.5

The structure of Tubulin-Z1891773393-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1891773393-Complex (pdb code 5s4l). 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-Z1891773393-Complex, PDB code: 5s4l:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1891773393-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1891773393-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:86.0 occ:1.00 O A:GLY44 2.3 91.1 1.0 OE2 A:GLU55 2.4 82.3 1.0 OD2 A:ASP39 2.4 82.9 1.0 O A:HOH624 2.4 85.7 1.0 OD1 A:ASP39 2.5 88.9 1.0 O A:THR41 2.6 97.1 1.0 OG1 A:THR41 2.7 89.1 1.0 OE1 A:GLU55 2.7 89.5 1.0 CG A:ASP39 2.8 86.4 1.0 CD A:GLU55 2.9 85.8 1.0 C A:GLY44 3.3 93.2 1.0 CB A:THR41 3.5 89.5 1.0 C A:THR41 3.6 97.2 1.0 CA A:THR41 4.0 99.6 1.0 N A:GLY45 4.0 91.1 1.0 CA A:GLY45 4.0 95.5 1.0 N A:GLY44 4.2 92.8 1.0 CZ A:PHE49 4.2 77.1 1.0 CB A:ASP39 4.3 87.4 1.0 N A:THR41 4.3 98.9 1.0 CA A:GLY44 4.3 93.8 1.0 CG A:GLU55 4.4 79.6 1.0 OD1 A:ASN50 4.4 84.1 1.0 OD2 A:ASP47 4.6 85.0 1.0 ND2 A:ASN50 4.7 78.2 1.0 CE1 A:PHE49 4.8 76.9 1.0 NE2 A:HIS61 4.8 80.6 1.0 N A:ILE42 4.8 95.2 1.0 CG2 A:THR41 4.9 85.2 1.0 C A:GLY45 4.9 95.0 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1891773393-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1891773393-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:93.5 occ:1.00 O A:HOH652 3.0 71.9 1.0 O A:HOH602 3.4 66.9 1.0 OD2 E:ASP44 3.5 99.6 1.0 OG A:SER158 3.7 68.2 1.0 CB A:SER158 3.9 66.0 1.0 NZ A:LYS166 4.0 67.8 1.0 O A:GLY162 4.3 83.1 1.0 O A:HOH647 4.4 79.4 1.0 O A:GLU196 4.6 72.7 1.0 CA A:SER158 4.7 66.0 1.0 CG E:ASP44 4.7 95.5 1.0 O A:HIS197 4.9 65.5 1.0 CA A:HIS197 4.9 67.2 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1891773393-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1891773393-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:117.1 occ:1.00 OE1 B:GLU113 2.8 78.2 1.0 CD B:GLU113 3.8 78.5 1.0 OE2 B:GLU113 4.0 79.8 1.0 OE1 B:GLU110 4.1 61.5 1.0 CD B:GLU110 5.0 62.5 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1891773393-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1891773393-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:68.5 occ:1.00 O C:GLY44 2.3 77.1 1.0 OE1 C:GLU55 2.3 64.5 1.0 OG1 C:THR41 2.4 74.3 1.0 OD2 C:ASP39 2.4 62.0 1.0 OE2 C:GLU55 2.5 62.3 1.0 O C:THR41 2.5 69.4 1.0 OD1 C:ASP39 2.6 68.2 1.0 O C:HOH602 2.7 60.8 1.0 CD C:GLU55 2.7 66.4 1.0 CG C:ASP39 2.9 65.6 1.0 CB C:THR41 3.4 75.4 1.0 C C:THR41 3.4 73.6 1.0 C C:GLY44 3.5 78.4 1.0 CA C:THR41 3.8 74.7 1.0 N C:THR41 4.1 72.2 1.0 CA C:GLY45 4.2 72.1 1.0 CG C:GLU55 4.2 60.8 1.0 N C:GLY45 4.2 77.9 1.0 N C:GLY44 4.3 82.2 1.0 CB C:ASP39 4.4 64.7 1.0 OD2 C:ASP47 4.4 71.6 1.0 CA C:GLY44 4.5 80.1 1.0 N C:ILE42 4.6 72.6 1.0 NE2 C:HIS61 4.6 56.7 1.0 CZ C:PHE49 4.7 53.3 1.0 OD1 C:ASN50 4.7 59.4 1.0 CG2 C:THR41 4.7 63.8 1.0 ND2 C:ASN50 4.9 57.6 1.0 O C:HOH742 5.0 68.4 1.0 CB C:GLU55 5.0 58.1 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