Calcium in PDB 5s5x: Tubulin-Z45705015-Complex

The structure of Tubulin-Z45705015-Complex, PDB code: 5s5x 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)	63.41 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.96, 159.13, 178.6, 90, 90, 90
R / Rfree (%)	20.7 / 24.3

The structure of Tubulin-Z45705015-Complex also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Tubulin-Z45705015-Complex (pdb code 5s5x). 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-Z45705015-Complex, PDB code: 5s5x:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z45705015-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z45705015-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:86.9 occ:1.00 O A:GLY44 2.2 88.8 1.0 OD2 A:ASP39 2.4 78.8 1.0 OD1 A:ASP39 2.4 91.9 1.0 OG1 A:THR41 2.5 87.8 1.0 O A:HOH607 2.5 80.5 1.0 OE2 A:GLU55 2.6 80.3 1.0 O A:THR41 2.6 88.4 1.0 CG A:ASP39 2.7 85.5 1.0 OE1 A:GLU55 2.9 84.5 1.0 CD A:GLU55 3.1 81.1 1.0 C A:GLY44 3.4 90.5 1.0 CB A:THR41 3.5 90.0 1.0 C A:THR41 3.6 90.2 1.0 CA A:THR41 4.0 95.2 1.0 CA A:GLY45 4.1 94.3 1.0 N A:GLY45 4.2 90.0 1.0 CB A:ASP39 4.2 86.1 1.0 N A:THR41 4.3 93.6 1.0 N A:GLY44 4.3 88.4 1.0 CZ A:PHE49 4.4 75.7 1.0 OD2 A:ASP47 4.5 84.9 1.0 CA A:GLY44 4.5 89.7 1.0 OD1 A:ASN50 4.5 83.7 1.0 CG A:GLU55 4.6 76.4 1.0 NE2 A:HIS61 4.7 78.6 1.0 ND2 A:ASN50 4.8 76.3 1.0 CG2 A:THR41 4.8 82.5 1.0 N A:ILE42 4.8 87.9 1.0 CE1 A:PHE49 4.9 74.8 1.0 C A:GLY45 5.0 94.1 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z45705015-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z45705015-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:97.3 occ:1.00 O E:HOH204 2.6 81.8 1.0 O A:HOH659 3.0 70.7 1.0 O A:HOH623 3.5 64.4 1.0 OD2 E:ASP44 3.7 109.9 1.0 OG A:SER158 3.8 71.8 1.0 CB A:SER158 4.2 68.6 1.0 NZ A:LYS166 4.2 64.1 1.0 O A:GLY162 4.3 92.1 1.0 O A:GLU196 4.4 70.5 1.0 O A:HIS197 4.7 68.3 1.0 CA A:HIS197 4.7 67.5 1.0 CG E:ASP44 4.7 107.9 1.0 CA A:SER158 4.9 66.3 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z45705015-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z45705015-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:104.1 occ:1.00 OE1 B:GLU113 2.5 82.3 1.0 CD B:GLU113 3.3 81.4 1.0 OE2 B:GLU113 3.4 80.9 1.0 OE1 B:GLU110 4.6 53.0 1.0 CG B:GLU113 4.8 69.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z45705015-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z45705015-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:71.3 occ:1.00 O C:GLY44 2.4 66.4 1.0 OE1 C:GLU55 2.4 71.2 1.0 O C:THR41 2.4 71.3 1.0 OG1 C:THR41 2.5 76.4 1.0 OE2 C:GLU55 2.5 63.9 1.0 OD1 C:ASP39 2.5 72.7 1.0 OD2 C:ASP39 2.5 64.7 1.0 O C:HOH602 2.6 63.3 1.0 CD C:GLU55 2.8 64.5 1.0 CG C:ASP39 2.8 68.0 1.0 C C:THR41 3.4 74.7 1.0 CB C:THR41 3.5 76.3 1.0 C C:GLY44 3.5 73.5 1.0 CA C:THR41 3.9 75.5 1.0 N C:THR41 4.2 77.0 1.0 CA C:GLY45 4.2 74.1 1.0 CG C:GLU55 4.3 62.4 1.0 N C:GLY45 4.3 74.8 1.0 OD2 C:ASP47 4.3 74.8 1.0 CB C:ASP39 4.3 69.7 1.0 N C:GLY44 4.4 73.8 1.0 CA C:GLY44 4.5 74.3 1.0 CZ C:PHE49 4.6 58.6 1.0 OD1 C:ASN50 4.6 64.1 1.0 N C:ILE42 4.6 74.3 1.0 NE2 C:HIS61 4.6 56.9 1.0 CG2 C:THR41 4.8 65.0 1.0 O C:HOH709 4.9 66.0 1.0 ND2 C:ASN50 4.9 56.5 1.0 CE1 C:PHE49 5.0 58.9 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