Calcium in PDB 5s4t: Tubulin-Z328695024-Complex

The structure of Tubulin-Z328695024-Complex, PDB code: 5s4t 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)	62.53 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.77, 158.42, 179.05, 90, 90, 90
R / Rfree (%)	20.6 / 24.6

The structure of Tubulin-Z328695024-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z328695024-Complex (pdb code 5s4t). 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-Z328695024-Complex, PDB code: 5s4t:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z328695024-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z328695024-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:91.3 occ:1.00 O A:GLY44 2.3 94.3 1.0 OD1 A:ASP39 2.3 90.9 1.0 OD2 A:ASP39 2.4 87.2 1.0 O A:HOH605 2.5 88.5 1.0 O A:THR41 2.5 100.1 1.0 OG1 A:THR41 2.5 91.8 1.0 OE1 A:GLU55 2.5 91.6 1.0 OE2 A:GLU55 2.6 85.0 1.0 CG A:ASP39 2.7 90.7 1.0 CD A:GLU55 2.9 89.3 1.0 CB A:THR41 3.4 97.9 1.0 C A:GLY44 3.5 98.7 1.0 C A:THR41 3.5 99.8 1.0 CA A:THR41 3.9 102.0 1.0 CA A:GLY45 4.1 101.5 1.0 N A:THR41 4.2 101.1 1.0 CB A:ASP39 4.2 92.0 1.0 N A:GLY45 4.2 97.9 1.0 CZ A:PHE49 4.3 79.8 1.0 N A:GLY44 4.4 96.6 1.0 CG A:GLU55 4.4 86.9 1.0 OD1 A:ASN50 4.5 88.6 1.0 CA A:GLY44 4.5 99.8 1.0 OD2 A:ASP47 4.5 91.8 1.0 N A:ILE42 4.7 102.0 1.0 CG2 A:THR41 4.8 92.9 1.0 CE1 A:PHE49 4.8 81.6 1.0 ND2 A:ASN50 4.9 84.3 1.0 NE2 A:HIS61 4.9 88.3 1.0 CA A:ASP39 4.9 94.2 1.0 C A:ASP39 5.0 100.6 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z328695024-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z328695024-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:106.1 occ:1.00 OE1 B:GLU113 2.5 88.8 1.0 CD B:GLU113 3.3 88.7 1.0 OE2 B:GLU113 3.4 90.4 1.0 OE1 B:GLU110 4.4 61.0 1.0 CG B:GLU113 4.8 74.7 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z328695024-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z328695024-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:72.5 occ:1.00 OD2 C:ASP39 2.4 68.4 1.0 O C:GLY44 2.4 74.3 1.0 OE1 C:GLU55 2.5 71.0 1.0 O C:THR41 2.5 73.1 1.0 OE2 C:GLU55 2.5 66.9 1.0 OD1 C:ASP39 2.5 70.1 1.0 O C:HOH602 2.5 65.2 1.0 OG1 C:THR41 2.6 75.3 1.0 CG C:ASP39 2.8 68.2 1.0 CD C:GLU55 2.8 68.1 1.0 C C:THR41 3.5 76.8 1.0 CB C:THR41 3.6 79.2 1.0 C C:GLY44 3.6 79.2 1.0 CA C:THR41 4.0 76.9 1.0 OD2 C:ASP47 4.2 75.6 1.0 N C:THR41 4.2 77.3 1.0 CB C:ASP39 4.3 74.2 1.0 CA C:GLY45 4.3 79.7 1.0 CG C:GLU55 4.3 67.4 1.0 N C:GLY45 4.4 82.7 1.0 CZ C:PHE49 4.5 59.1 1.0 OD1 C:ASN50 4.5 65.4 1.0 N C:GLY44 4.6 81.5 1.0 NE2 C:HIS61 4.7 59.0 1.0 CA C:GLY44 4.7 77.8 1.0 N C:ILE42 4.7 77.8 1.0 ND2 C:ASN50 4.9 60.5 1.0 O C:HOH694 4.9 70.4 1.0 CG2 C:THR41 4.9 67.6 1.0 CE1 C:PHE49 4.9 61.1 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z328695024-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z328695024-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:101.3 occ:1.00 O A:HOH644 2.3 76.2 1.0 O A:HOH653 3.1 74.3 1.0 OD2 E:ASP44 3.4 119.9 1.0 O A:HOH636 3.7 65.0 1.0 O A:GLU196 3.8 77.9 1.0 OG A:SER158 4.0 73.0 1.0 CA A:HIS197 4.5 72.3 1.0 CG E:ASP44 4.5 119.6 1.0 CB A:SER158 4.5 68.4 1.0 NZ A:LYS166 4.5 71.7 1.0 O A:HIS197 4.7 70.0 1.0 OD1 E:ASP44 4.8 117.3 1.0 C A:GLU196 4.8 71.4 1.0 ND1 A:HIS197 4.8 75.5 1.0 C A:HIS197 4.9 72.4 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