Calcium in PDB 5s4q: Tubulin-Z422344882-Complex

The structure of Tubulin-Z422344882-Complex, PDB code: 5s4q 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)	118.76 / 2.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.743, 158.302, 179.614, 90, 90, 90
R / Rfree (%)	22.6 / 28.2

The structure of Tubulin-Z422344882-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z422344882-Complex (pdb code 5s4q). 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-Z422344882-Complex, PDB code: 5s4q:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z422344882-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z422344882-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:76.9 occ:1.00 OE2 A:GLU55 2.3 71.7 1.0 O A:GLY44 2.3 77.2 1.0 OD1 A:ASP39 2.5 70.2 1.0 OD2 A:ASP39 2.5 71.1 1.0 O A:THR41 2.6 81.7 1.0 OG1 A:THR41 2.7 80.1 1.0 CG A:ASP39 2.8 72.8 1.0 OE1 A:GLU55 2.9 80.0 1.0 CD A:GLU55 2.9 78.6 1.0 C A:GLY44 3.5 73.7 1.0 CB A:THR41 3.5 78.0 1.0 C A:THR41 3.6 83.4 1.0 OD2 A:ASP47 4.0 78.1 1.0 CA A:THR41 4.0 80.1 1.0 CA A:GLY45 4.0 79.2 1.0 CZ A:PHE49 4.2 72.0 1.0 N A:GLY45 4.2 72.4 1.0 OD1 A:ASN50 4.3 65.7 1.0 N A:THR41 4.3 78.3 1.0 CB A:ASP39 4.3 70.5 1.0 CG A:GLU55 4.4 77.7 1.0 N A:GLY44 4.5 75.4 1.0 CA A:GLY44 4.6 77.5 1.0 CE1 A:PHE49 4.7 71.5 1.0 ND2 A:ASN50 4.7 68.0 1.0 NE2 A:HIS61 4.8 78.9 1.0 N A:ILE42 4.8 83.7 1.0 CG2 A:THR41 4.9 68.1 1.0 C A:GLY45 4.9 77.0 1.0 CG A:ASN50 5.0 64.6 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z422344882-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z422344882-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:87.5 occ:1.00 O E:HOH202 2.4 70.9 1.0 O A:HOH604 2.7 54.3 1.0 O A:HOH631 3.8 65.8 1.0 OD2 E:ASP44 3.8 79.8 1.0 NZ A:LYS166 3.9 59.5 1.0 OG A:SER158 4.1 65.6 1.0 O A:GLY162 4.4 65.8 1.0 CB A:SER158 4.4 56.8 1.0 OD1 A:ASP199 4.6 56.2 1.0 O A:GLU196 4.7 68.1 1.0 O A:HIS197 4.8 54.0 1.0 CA A:SER158 5.0 59.7 1.0 CG E:ASP44 5.0 86.7 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z422344882-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z422344882-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:72.9 occ:1.00 OE1 B:GLU113 2.6 62.1 1.0 CD B:GLU113 3.4 63.2 1.0 OE2 B:GLU113 3.4 65.9 1.0 OE1 B:GLU110 4.6 47.0 1.0 CG B:GLU113 4.8 48.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z422344882-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z422344882-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:56.7 occ:1.00 O C:GLY44 2.4 58.0 1.0 O C:THR41 2.4 60.9 1.0 OG1 C:THR41 2.4 62.6 1.0 OD2 C:ASP39 2.6 50.5 1.0 OE2 C:GLU55 2.6 54.0 1.0 OD1 C:ASP39 2.6 58.2 1.0 O C:HOH608 2.6 52.8 1.0 OE1 C:GLU55 2.7 57.2 1.0 CG C:ASP39 2.9 52.9 1.0 CD C:GLU55 3.0 54.4 1.0 CB C:THR41 3.4 53.4 1.0 C C:THR41 3.4 61.2 1.0 C C:GLY44 3.6 61.8 1.0 CA C:THR41 3.8 54.7 1.0 OD2 C:ASP47 4.2 59.8 1.0 N C:THR41 4.2 56.6 1.0 CA C:GLY45 4.2 58.0 1.0 N C:GLY45 4.3 68.1 1.0 CB C:ASP39 4.4 52.8 1.0 CG C:GLU55 4.5 45.4 1.0 OD1 C:ASN50 4.5 55.3 1.0 N C:ILE42 4.6 57.7 1.0 N C:GLY44 4.6 62.9 1.0 CA C:GLY44 4.6 60.4 1.0 CZ C:PHE49 4.6 47.5 1.0 CG2 C:THR41 4.7 50.9 1.0 ND2 C:ASN50 4.8 48.3 1.0 CE1 C:PHE49 5.0 42.2 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