Calcium in PDB 5s4p: Tubulin-Z275165822-Complex

The structure of Tubulin-Z275165822-Complex, PDB code: 5s4p 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)	78.52 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.246, 157.049, 178.157, 90, 90, 90
R / Rfree (%)	20.8 / 24.4

The structure of Tubulin-Z275165822-Complex also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Calcium atom in the Tubulin-Z275165822-Complex (pdb code 5s4p). 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-Z275165822-Complex, PDB code: 5s4p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z275165822-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z275165822-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:73.6 occ:1.00 O A:GLY44 2.3 79.1 1.0 OD2 A:ASP39 2.3 70.1 1.0 O A:HOH634 2.4 71.8 1.0 OD1 A:ASP39 2.4 75.6 1.0 O A:THR41 2.4 83.1 1.0 OE2 A:GLU55 2.5 69.1 1.0 OE1 A:GLU55 2.5 73.5 1.0 OG1 A:THR41 2.6 76.2 1.0 CG A:ASP39 2.7 71.1 1.0 CD A:GLU55 2.9 72.1 1.0 C A:THR41 3.4 84.8 1.0 C A:GLY44 3.4 82.8 1.0 CB A:THR41 3.5 79.3 1.0 CA A:THR41 3.9 80.6 1.0 CA A:GLY45 4.2 88.1 1.0 CB A:ASP39 4.2 69.5 1.0 N A:THR41 4.2 84.2 1.0 N A:GLY45 4.2 85.8 1.0 N A:GLY44 4.3 82.3 1.0 CG A:GLU55 4.4 67.5 1.0 CZ A:PHE49 4.4 66.8 1.0 CA A:GLY44 4.5 78.3 1.0 N A:ILE42 4.6 87.4 1.0 OD1 A:ASN50 4.6 75.9 1.0 OD2 A:ASP47 4.7 73.9 1.0 NE2 A:HIS61 4.7 67.8 1.0 ND2 A:ASN50 4.9 65.0 1.0 CG2 A:THR41 4.9 76.3 1.0 CA A:ILE42 5.0 86.1 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z275165822-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z275165822-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:84.6 occ:1.00 O A:HOH656 2.5 66.0 1.0 OD2 E:ASP44 3.5 94.2 1.0 O A:HOH629 3.6 50.2 1.0 O A:GLU196 3.8 58.1 1.0 OG A:SER158 4.0 54.6 1.0 CA A:HIS197 4.4 50.7 1.0 NZ A:LYS166 4.4 51.7 1.0 CB A:SER158 4.5 54.8 1.0 O A:HIS197 4.5 53.8 1.0 CG E:ASP44 4.6 93.9 1.0 C A:HIS197 4.7 50.0 1.0 OD1 A:ASP199 4.8 60.3 1.0 OD1 E:ASP44 4.8 92.1 1.0 C A:GLU196 4.8 52.8 1.0 ND1 A:HIS197 5.0 56.2 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z275165822-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z275165822-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:95.3 occ:1.00 OE1 B:GLU113 2.4 69.8 1.0 CD B:GLU113 3.3 70.4 1.0 OE2 B:GLU113 3.6 71.7 1.0 OE1 B:GLU110 4.2 50.2 1.0 CG B:GLU113 4.7 55.6 1.0 CD B:GLU110 5.0 51.6 1.0 CB B:GLU113 5.0 50.0 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z275165822-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z275165822-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:59.1 occ:1.00 OD2 C:ASP39 2.3 60.1 1.0 O C:GLY44 2.4 65.9 1.0 O C:HOH602 2.4 55.4 1.0 OE2 C:GLU55 2.5 62.9 1.0 O C:THR41 2.5 62.6 1.0 OD1 C:ASP39 2.5 61.1 1.0 OG1 C:THR41 2.5 63.4 1.0 OE1 C:GLU55 2.6 59.4 1.0 CG C:ASP39 2.8 58.3 1.0 CD C:GLU55 2.9 62.7 1.0 CB C:THR41 3.5 65.8 1.0 C C:THR41 3.5 70.4 1.0 C C:GLY44 3.5 68.6 1.0 CA C:THR41 3.9 67.4 1.0 CA C:GLY45 4.1 68.3 1.0 OD2 C:ASP47 4.2 65.2 1.0 N C:GLY45 4.2 70.2 1.0 N C:THR41 4.2 71.0 1.0 CB C:ASP39 4.3 59.6 1.0 CG C:GLU55 4.4 55.1 1.0 CZ C:PHE49 4.4 53.2 1.0 N C:GLY44 4.5 72.7 1.0 OD1 C:ASN50 4.6 58.0 1.0 CA C:GLY44 4.6 69.7 1.0 N C:ILE42 4.7 67.0 1.0 NE2 C:HIS61 4.7 54.2 1.0 ND2 C:ASN50 4.8 51.5 1.0 CG2 C:THR41 4.8 55.4 1.0 O C:HOH739 4.9 60.5 1.0 CE1 C:PHE49 5.0 55.3 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