Calcium in PDB 5s5g: Tubulin-Z1129283193-Complex

The structure of Tubulin-Z1129283193-Complex, PDB code: 5s5g 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)	72.26 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.645, 157.922, 179.187, 90, 90, 90
R / Rfree (%)	21.8 / 27.1

The structure of Tubulin-Z1129283193-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1129283193-Complex (pdb code 5s5g). 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-Z1129283193-Complex, PDB code: 5s5g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1129283193-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1129283193-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:72.3 occ:1.00 OG1 A:THR41 2.3 89.5 1.0 O A:GLY44 2.4 77.7 1.0 OE2 A:GLU55 2.4 76.7 1.0 OD1 A:ASP39 2.6 72.7 1.0 OD2 A:ASP39 2.7 61.9 1.0 O A:THR41 2.7 84.7 1.0 CG A:ASP39 2.9 64.4 1.0 OE1 A:GLU55 3.0 77.2 1.0 CD A:GLU55 3.0 73.3 1.0 C A:GLY44 3.4 77.9 1.0 CB A:THR41 3.4 83.8 1.0 C A:THR41 3.7 87.0 1.0 CA A:GLY45 3.9 86.1 1.0 OD1 A:ASN50 4.0 69.9 1.0 CA A:THR41 4.0 85.2 1.0 N A:GLY45 4.1 73.2 1.0 OD2 A:ASP47 4.1 66.0 1.0 N A:THR41 4.3 85.8 1.0 CZ A:PHE49 4.3 53.2 1.0 CB A:ASP39 4.4 64.2 1.0 CG A:GLU55 4.5 69.6 1.0 CA A:GLY44 4.5 79.0 1.0 N A:GLY44 4.5 77.8 1.0 ND2 A:ASN50 4.7 58.6 1.0 C A:GLY45 4.7 87.5 1.0 CG2 A:THR41 4.7 78.7 1.0 CG A:ASN50 4.8 62.8 1.0 CE1 A:PHE49 4.9 50.0 1.0 N A:ILE42 4.9 88.8 1.0 O A:GLY45 5.0 82.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1129283193-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1129283193-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:70.4 occ:1.00 O E:HOH202 2.3 58.0 1.0 O A:HOH643 3.3 38.6 1.0 OD2 E:ASP44 3.7 73.9 1.0 OG A:SER158 3.9 44.9 1.0 O A:GLY162 4.0 67.2 1.0 CB A:SER158 4.2 46.3 1.0 NZ A:LYS166 4.2 43.9 1.0 O A:GLU196 4.7 44.5 1.0 CA A:SER158 4.8 46.6 1.0 OD1 A:ASP199 4.9 47.7 1.0 CG E:ASP44 4.9 75.4 1.0 O A:LYS164 4.9 54.6 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1129283193-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1129283193-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:81.5 occ:1.00 OE1 B:GLU113 2.4 73.4 1.0 CD B:GLU113 3.3 69.8 1.0 OE2 B:GLU113 3.3 60.5 1.0 OE1 B:GLU110 4.2 42.7 1.0 CG B:GLU113 4.7 55.6 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1129283193-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1129283193-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:46.6 occ:1.00 OE1 C:GLU55 2.3 48.5 1.0 OE2 C:GLU55 2.4 43.1 1.0 O C:HOH604 2.4 45.6 1.0 O C:THR41 2.4 53.1 1.0 O C:GLY44 2.5 48.4 1.0 OD2 C:ASP39 2.5 43.7 1.0 OG1 C:THR41 2.5 51.2 1.0 CD C:GLU55 2.7 45.6 1.0 OD1 C:ASP39 2.7 46.7 1.0 CG C:ASP39 2.9 45.2 1.0 C C:THR41 3.4 52.5 1.0 CB C:THR41 3.5 49.7 1.0 C C:GLY44 3.6 49.9 1.0 CA C:THR41 3.9 50.1 1.0 CG C:GLU55 4.2 41.5 1.0 N C:THR41 4.3 48.0 1.0 CA C:GLY45 4.3 63.2 1.0 N C:GLY45 4.3 58.1 1.0 OD2 C:ASP47 4.4 55.2 1.0 CB C:ASP39 4.4 43.9 1.0 OD1 C:ASN50 4.5 46.5 1.0 N C:GLY44 4.5 51.5 1.0 CZ C:PHE49 4.6 38.6 1.0 N C:ILE42 4.6 55.6 1.0 CA C:GLY44 4.6 49.3 1.0 NE2 C:HIS61 4.6 38.0 1.0 O C:HOH723 4.8 43.3 1.0 ND2 C:ASN50 4.8 42.1 1.0 CG2 C:THR41 4.8 42.5 1.0 CE1 C:PHE49 4.9 38.5 1.0 CB C:GLU55 5.0 37.3 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