Calcium in PDB 5s67: Tubulin-Z1896597864-Complex

The structure of Tubulin-Z1896597864-Complex, PDB code: 5s67 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)	62.75 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.9, 158.96, 179.98, 90, 90, 90
R / Rfree (%)	21 / 23.8

The structure of Tubulin-Z1896597864-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1896597864-Complex (pdb code 5s67). 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-Z1896597864-Complex, PDB code: 5s67:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1896597864-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1896597864-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:84.3 occ:1.00 O A:GLY44 2.3 88.5 1.0 OD2 A:ASP39 2.3 87.6 1.0 OE2 A:GLU55 2.4 81.0 1.0 OD1 A:ASP39 2.5 86.7 1.0 OG1 A:THR41 2.6 88.9 1.0 O A:THR41 2.6 94.5 1.0 CG A:ASP39 2.7 88.6 1.0 OE1 A:GLU55 2.7 90.4 1.0 CD A:GLU55 2.9 90.1 1.0 C A:GLY44 3.4 92.8 1.0 CB A:THR41 3.6 93.6 1.0 C A:THR41 3.6 98.6 1.0 CA A:GLY45 4.0 91.6 1.0 CA A:THR41 4.0 97.4 1.0 N A:GLY45 4.1 95.0 1.0 CZ A:PHE49 4.2 82.5 1.0 CB A:ASP39 4.2 90.5 1.0 N A:THR41 4.3 99.0 1.0 N A:GLY44 4.4 95.0 1.0 CG A:GLU55 4.4 84.4 1.0 OD2 A:ASP47 4.4 80.5 1.0 CA A:GLY44 4.4 96.5 1.0 OD1 A:ASN50 4.5 87.5 1.0 ND2 A:ASN50 4.7 80.6 1.0 NE2 A:HIS61 4.8 87.0 1.0 N A:ILE42 4.8 101.0 1.0 CE1 A:PHE49 4.9 76.5 1.0 CG2 A:THR41 4.9 83.4 1.0 C A:GLY45 4.9 88.3 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1896597864-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1896597864-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:91.5 occ:1.00 O E:HOH701 2.5 82.3 1.0 O A:HOH664 3.1 69.8 1.0 O A:HOH626 3.2 63.1 1.0 O A:HOH607 3.7 71.6 1.0 OG A:SER158 3.7 69.8 1.0 OD2 E:ASP44 3.8 100.9 1.0 NZ A:LYS166 4.0 60.6 1.0 CB A:SER158 4.1 68.7 1.0 O A:GLY162 4.3 87.9 1.0 O A:GLU196 4.7 69.3 1.0 O A:HIS197 4.7 61.2 1.0 CA A:SER158 4.8 67.0 1.0 CA A:HIS197 4.9 65.0 1.0 CG E:ASP44 5.0 99.6 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1896597864-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1896597864-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:110.7 occ:1.00 OE1 B:GLU113 2.7 70.5 1.0 CD B:GLU113 3.7 73.4 1.0 OE2 B:GLU113 3.9 79.8 1.0 OE1 B:GLU110 4.0 56.4 1.0 CD B:GLU110 4.8 60.4 1.0 OE2 B:GLU110 4.8 69.4 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1896597864-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1896597864-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:66.1 occ:1.00 O C:GLY44 2.4 74.7 1.0 OE1 C:GLU55 2.4 62.1 1.0 OD2 C:ASP39 2.4 59.0 1.0 O C:THR41 2.4 65.8 1.0 OE2 C:GLU55 2.5 59.2 1.0 O C:HOH604 2.5 57.8 1.0 OG1 C:THR41 2.6 67.8 1.0 OD1 C:ASP39 2.6 65.4 1.0 CD C:GLU55 2.8 62.8 1.0 CG C:ASP39 2.9 64.6 1.0 C C:THR41 3.4 74.4 1.0 CB C:THR41 3.5 73.7 1.0 C C:GLY44 3.5 75.9 1.0 CA C:THR41 3.9 71.7 1.0 N C:THR41 4.2 71.1 1.0 CG C:GLU55 4.3 58.5 1.0 OD2 C:ASP47 4.3 68.6 1.0 N C:GLY44 4.4 78.8 1.0 CB C:ASP39 4.4 69.9 1.0 CA C:GLY45 4.4 73.1 1.0 N C:GLY45 4.4 78.3 1.0 CA C:GLY44 4.5 76.3 1.0 OD1 C:ASN50 4.5 60.9 1.0 CZ C:PHE49 4.6 53.0 1.0 N C:ILE42 4.6 72.8 1.0 NE2 C:HIS61 4.7 57.5 1.0 CG2 C:THR41 4.9 58.9 1.0 ND2 C:ASN50 4.9 57.5 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