Calcium in PDB 5s5s: Tubulin-Z166605480-Complex

The structure of Tubulin-Z166605480-Complex, PDB code: 5s5s 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 / 2.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.55, 158.051, 179.339, 90, 90, 90
R / Rfree (%)	21.2 / 25.4

The structure of Tubulin-Z166605480-Complex also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Tubulin-Z166605480-Complex (pdb code 5s5s). 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-Z166605480-Complex, PDB code: 5s5s:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z166605480-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z166605480-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:75.9 occ:1.00 O A:GLY44 2.3 78.3 1.0 OD1 A:ASP39 2.4 81.2 1.0 OD2 A:ASP39 2.4 73.9 1.0 OE2 A:GLU55 2.4 72.6 1.0 OG1 A:THR41 2.4 80.9 1.0 O A:THR41 2.6 84.6 1.0 CG A:ASP39 2.7 77.6 1.0 OE1 A:GLU55 2.9 76.4 1.0 CD A:GLU55 3.0 74.1 1.0 C A:GLY44 3.4 80.3 1.0 CB A:THR41 3.5 80.3 1.0 C A:THR41 3.6 86.0 1.0 CA A:GLY45 4.0 79.1 1.0 CA A:THR41 4.0 85.0 1.0 N A:GLY45 4.1 80.2 1.0 CZ A:PHE49 4.1 64.7 1.0 CB A:ASP39 4.2 77.1 1.0 OD2 A:ASP47 4.3 71.0 1.0 N A:THR41 4.3 88.4 1.0 OD1 A:ASN50 4.4 71.5 1.0 N A:GLY44 4.4 79.8 1.0 CA A:GLY44 4.5 81.3 1.0 CG A:GLU55 4.5 71.8 1.0 CE1 A:PHE49 4.6 64.5 1.0 ND2 A:ASN50 4.7 64.9 1.0 CG2 A:THR41 4.8 73.5 1.0 C A:GLY45 4.8 79.2 1.0 NE2 A:HIS61 4.8 71.4 1.0 N A:ILE42 4.9 86.4 1.0 CA A:ASP39 5.0 80.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z166605480-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z166605480-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:78.2 occ:1.00 O A:HOH659 2.9 57.1 1.0 O A:HOH639 3.3 50.8 1.0 OD2 E:ASP44 3.7 92.5 1.0 OG A:SER158 3.8 55.2 1.0 O A:GLY162 4.1 67.7 1.0 CB A:SER158 4.2 54.5 1.0 NZ A:LYS166 4.2 48.8 1.0 O A:GLU196 4.8 55.2 1.0 CG E:ASP44 4.8 90.3 1.0 CA A:SER158 4.8 55.7 1.0 O A:HIS197 4.9 49.4 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z166605480-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z166605480-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:88.9 occ:1.00 OE1 B:GLU113 2.6 67.3 1.0 CD B:GLU113 3.5 66.2 1.0 OE2 B:GLU113 3.7 65.8 1.0 OE1 B:GLU110 4.7 39.2 1.0 CG B:GLU113 4.9 54.9 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z166605480-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z166605480-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:56.6 occ:1.00 O C:GLY44 2.3 55.5 1.0 OE2 C:GLU55 2.4 51.1 1.0 O C:THR41 2.4 61.7 1.0 OD2 C:ASP39 2.4 52.2 1.0 O C:HOH601 2.5 50.9 1.0 OG1 C:THR41 2.5 60.5 1.0 OE1 C:GLU55 2.5 55.0 1.0 OD1 C:ASP39 2.6 56.0 1.0 CD C:GLU55 2.8 51.9 1.0 CG C:ASP39 2.8 55.0 1.0 C C:THR41 3.4 65.9 1.0 CB C:THR41 3.5 63.9 1.0 C C:GLY44 3.5 56.9 1.0 CA C:THR41 3.9 64.2 1.0 OD2 C:ASP47 4.1 57.9 1.0 CA C:GLY45 4.2 64.2 1.0 N C:THR41 4.2 63.2 1.0 CG C:GLU55 4.3 49.1 1.0 N C:GLY45 4.3 64.4 1.0 CB C:ASP39 4.3 52.3 1.0 CZ C:PHE49 4.5 46.6 1.0 OD1 C:ASN50 4.5 52.1 1.0 O C:HOH749 4.6 54.0 1.0 N C:ILE42 4.6 69.1 1.0 N C:GLY44 4.6 60.3 1.0 NE2 C:HIS61 4.6 44.4 1.0 CA C:GLY44 4.6 57.9 1.0 CG2 C:THR41 4.8 59.8 1.0 ND2 C:ASN50 4.8 46.0 1.0 CE1 C:PHE49 4.9 45.9 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