Calcium in PDB 5s5q: Tubulin-Z396380540-Complex

The structure of Tubulin-Z396380540-Complex, PDB code: 5s5q 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)	90.42 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.85, 158.62, 178.62, 90, 90, 90
R / Rfree (%)	21.2 / 24.4

The structure of Tubulin-Z396380540-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z396380540-Complex (pdb code 5s5q). 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-Z396380540-Complex, PDB code: 5s5q:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z396380540-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z396380540-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:74.7 occ:1.00 O A:GLY44 2.2 76.1 1.0 OD2 A:ASP39 2.4 71.5 1.0 OD1 A:ASP39 2.4 77.7 1.0 O A:THR41 2.4 78.4 1.0 O A:HOH625 2.4 65.8 1.0 OE2 A:GLU55 2.5 66.7 1.0 OG1 A:THR41 2.5 73.5 1.0 OE1 A:GLU55 2.6 74.9 1.0 CG A:ASP39 2.8 72.5 1.0 CD A:GLU55 2.9 73.9 1.0 CB A:THR41 3.4 78.2 1.0 C A:GLY44 3.4 80.5 1.0 C A:THR41 3.5 81.3 1.0 CA A:THR41 3.8 80.6 1.0 CA A:GLY45 4.1 83.7 1.0 N A:THR41 4.1 81.1 1.0 N A:GLY45 4.2 84.5 1.0 CB A:ASP39 4.3 71.8 1.0 N A:GLY44 4.4 78.3 1.0 CZ A:PHE49 4.4 63.5 1.0 CG A:GLU55 4.4 68.8 1.0 CA A:GLY44 4.5 79.2 1.0 OD1 A:ASN50 4.6 67.9 1.0 N A:ILE42 4.7 78.9 1.0 OD2 A:ASP47 4.7 69.8 1.0 NE2 A:HIS61 4.8 72.2 1.0 CG2 A:THR41 4.8 71.2 1.0 ND2 A:ASN50 5.0 67.6 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z396380540-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z396380540-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:90.4 occ:1.00 O A:HOH676 2.3 70.5 1.0 O E:HOH201 2.4 75.5 1.0 O A:HOH663 2.7 62.4 1.0 O A:HOH642 3.4 58.8 1.0 O A:GLU196 3.8 58.0 1.0 OD2 E:ASP44 4.1 97.5 1.0 OG A:SER158 4.2 59.6 1.0 CA A:HIS197 4.4 55.4 1.0 NZ A:LYS166 4.5 56.2 1.0 OD1 A:ASP199 4.6 62.0 1.0 O A:HIS197 4.6 57.6 1.0 C A:HIS197 4.7 57.9 1.0 CB A:SER158 4.7 59.5 1.0 C A:GLU196 4.9 58.0 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z396380540-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z396380540-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:96.0 occ:1.00 OE1 B:GLU113 2.6 72.1 1.0 CD B:GLU113 3.5 67.9 1.0 OE2 B:GLU113 3.7 71.6 1.0 OE1 B:GLU110 4.6 45.6 1.0 CG B:GLU113 4.9 57.3 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z396380540-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z396380540-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:53.0 occ:1.00 OD2 C:ASP39 2.3 50.8 1.0 O C:GLY44 2.4 57.9 1.0 O C:HOH601 2.4 45.7 1.0 OE2 C:GLU55 2.4 50.8 1.0 OG1 C:THR41 2.4 55.2 1.0 OE1 C:GLU55 2.5 48.6 1.0 O C:THR41 2.5 52.7 1.0 OD1 C:ASP39 2.5 54.8 1.0 CG C:ASP39 2.8 53.0 1.0 CD C:GLU55 2.8 52.3 1.0 C C:GLY44 3.5 60.4 1.0 C C:THR41 3.5 56.5 1.0 CB C:THR41 3.5 60.7 1.0 CA C:THR41 4.0 57.1 1.0 OD2 C:ASP47 4.1 58.0 1.0 N C:THR41 4.2 57.4 1.0 CB C:ASP39 4.3 55.3 1.0 CG C:GLU55 4.3 47.3 1.0 CA C:GLY45 4.3 58.1 1.0 N C:GLY45 4.3 59.8 1.0 N C:GLY44 4.3 62.6 1.0 CA C:GLY44 4.5 60.8 1.0 CZ C:PHE49 4.5 49.7 1.0 OD1 C:ASN50 4.6 49.8 1.0 NE2 C:HIS61 4.6 48.6 1.0 N C:ILE42 4.7 59.3 1.0 CG2 C:THR41 4.8 54.4 1.0 ND2 C:ASN50 4.9 46.4 1.0 CE1 C:PHE49 5.0 50.8 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