Calcium in PDB 5s5t: Tubulin-Z198194394-Complex

The structure of Tubulin-Z198194394-Complex, PDB code: 5s5t 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)	72.32 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.834, 158.225, 178.442, 90, 90, 90
R / Rfree (%)	21.1 / 25.6

The structure of Tubulin-Z198194394-Complex also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Tubulin-Z198194394-Complex (pdb code 5s5t). 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-Z198194394-Complex, PDB code: 5s5t:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z198194394-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z198194394-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:80.4 occ:1.00 O A:GLY44 2.3 76.4 1.0 OD2 A:ASP39 2.3 69.5 1.0 OD1 A:ASP39 2.3 76.7 1.0 OE2 A:GLU55 2.4 73.8 1.0 O A:THR41 2.5 80.3 1.0 O A:HOH604 2.5 70.8 1.0 OG1 A:THR41 2.6 74.0 1.0 OE1 A:GLU55 2.6 75.0 1.0 CG A:ASP39 2.7 74.2 1.0 CD A:GLU55 2.8 74.1 1.0 C A:GLY44 3.4 78.1 1.0 C A:THR41 3.6 78.4 1.0 CB A:THR41 3.7 78.3 1.0 CA A:THR41 4.0 79.6 1.0 CB A:ASP39 4.2 73.6 1.0 CA A:GLY45 4.2 81.7 1.0 N A:GLY45 4.2 80.8 1.0 N A:GLY44 4.2 78.7 1.0 O A:HOH601 4.2 78.3 1.0 N A:THR41 4.3 81.0 1.0 CZ A:PHE49 4.3 64.9 1.0 CG A:GLU55 4.4 71.9 1.0 CA A:GLY44 4.4 77.0 1.0 OD1 A:ASN50 4.5 74.3 1.0 OD2 A:ASP47 4.6 73.0 1.0 N A:ILE42 4.7 80.7 1.0 NE2 A:HIS61 4.8 71.0 1.0 ND2 A:ASN50 4.8 66.0 1.0 CG2 A:THR41 4.9 74.5 1.0 CA A:ASP39 5.0 72.1 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z198194394-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z198194394-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:87.5 occ:1.00 OE1 B:GLU113 2.5 80.6 1.0 CD B:GLU113 3.3 77.6 1.0 OE2 B:GLU113 3.5 79.8 1.0 CG B:GLU113 4.7 63.0 1.0 OE1 B:GLU110 4.8 48.3 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z198194394-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z198194394-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:66.4 occ:1.00 O C:GLY44 2.2 73.5 1.0 OE2 C:GLU55 2.4 62.8 1.0 O C:HOH602 2.4 60.6 1.0 OD2 C:ASP39 2.5 60.0 1.0 O C:THR41 2.5 70.8 1.0 OE1 C:GLU55 2.6 67.4 1.0 OD1 C:ASP39 2.7 62.5 1.0 OG1 C:THR41 2.7 73.7 1.0 CD C:GLU55 2.8 64.0 1.0 CG C:ASP39 2.9 61.2 1.0 C C:GLY44 3.4 74.8 1.0 C C:THR41 3.5 71.8 1.0 CB C:THR41 3.5 68.9 1.0 CA C:THR41 4.0 70.1 1.0 CA C:GLY45 4.0 74.8 1.0 N C:GLY45 4.2 76.9 1.0 N C:THR41 4.3 73.8 1.0 CG C:GLU55 4.3 56.5 1.0 CB C:ASP39 4.4 65.1 1.0 OD2 C:ASP47 4.5 69.7 1.0 N C:GLY44 4.5 77.7 1.0 CA C:GLY44 4.6 76.5 1.0 OD1 C:ASN50 4.6 57.2 1.0 N C:ILE42 4.6 71.9 1.0 CZ C:PHE49 4.6 55.1 1.0 ND2 C:ASN50 4.7 53.4 1.0 NE2 C:HIS61 4.8 53.5 1.0 CG2 C:THR41 4.9 56.0 1.0 O C:HOH714 4.9 61.3 1.0 CE1 C:PHE49 5.0 56.4 1.0 C C:GLY45 5.0 75.9 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z198194394-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z198194394-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:80.3 occ:1.00 O A:HOH657 3.1 65.5 1.0 O A:HOH613 3.2 53.5 1.0 OD2 E:ASP44 3.4 94.0 1.0 OG A:SER158 3.9 56.5 1.0 O A:GLU196 4.0 57.7 1.0 O A:HOH658 4.0 68.3 1.0 CB A:SER158 4.4 57.5 1.0 NZ A:LYS166 4.4 46.8 1.0 CG E:ASP44 4.6 95.7 1.0 CA A:HIS197 4.6 55.4 1.0 O A:HIS197 4.7 53.9 1.0 O A:GLY162 4.9 83.0 1.0 C A:HIS197 4.9 55.7 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