Calcium in PDB 5s5o: Tubulin-Z27682767-Complex

The structure of Tubulin-Z27682767-Complex, PDB code: 5s5o 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)	62.74 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.25, 159.67, 179.23, 90, 90, 90
R / Rfree (%)	20.2 / 23.5

The structure of Tubulin-Z27682767-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z27682767-Complex (pdb code 5s5o). 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-Z27682767-Complex, PDB code: 5s5o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z27682767-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z27682767-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:89.3 occ:1.00 O A:GLY44 2.3 94.3 1.0 O A:HOH630 2.4 89.6 1.0 OD1 A:ASP39 2.4 94.4 1.0 OD2 A:ASP39 2.4 86.6 1.0 OE2 A:GLU55 2.4 89.2 1.0 OG1 A:THR41 2.5 90.2 1.0 O A:THR41 2.6 98.5 1.0 CG A:ASP39 2.7 90.2 1.0 OE1 A:GLU55 2.8 89.5 1.0 CD A:GLU55 2.9 90.3 1.0 C A:GLY44 3.4 95.8 1.0 CB A:THR41 3.5 93.8 1.0 C A:THR41 3.6 97.9 1.0 CA A:THR41 4.0 101.3 1.0 CA A:GLY45 4.1 98.6 1.0 N A:GLY45 4.1 94.2 1.0 CB A:ASP39 4.2 93.4 1.0 N A:THR41 4.3 100.5 1.0 CZ A:PHE49 4.3 79.9 1.0 N A:GLY44 4.3 96.3 1.0 CA A:GLY44 4.4 96.3 1.0 CG A:GLU55 4.4 86.4 1.0 OD2 A:ASP47 4.5 86.4 1.0 OD1 A:ASN50 4.6 85.8 1.0 ND2 A:ASN50 4.8 81.5 1.0 CG2 A:THR41 4.8 87.3 1.0 CE1 A:PHE49 4.8 78.4 1.0 N A:ILE42 4.8 101.9 1.0 NE2 A:HIS61 4.9 86.2 1.0 C A:GLY45 4.9 97.7 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z27682767-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z27682767-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:98.4 occ:1.00 O E:HOH201 2.7 86.8 1.0 O A:HOH656 3.0 74.9 1.0 O A:HOH605 3.4 67.9 1.0 OD2 E:ASP44 3.6 97.7 1.0 OG A:SER158 3.8 69.5 1.0 CB A:SER158 4.0 68.9 1.0 NZ A:LYS166 4.1 69.1 1.0 O A:GLY162 4.2 93.5 1.0 O A:GLU196 4.6 72.9 1.0 CA A:SER158 4.6 69.4 1.0 CG E:ASP44 4.8 104.5 1.0 CA A:HIS197 5.0 69.4 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z27682767-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z27682767-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:121.3 occ:1.00 OE1 B:GLU113 2.9 93.5 1.0 CD B:GLU113 3.7 89.2 1.0 OE2 B:GLU113 3.8 91.9 1.0 OE1 B:GLU110 4.6 60.7 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z27682767-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z27682767-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca604 b:69.3 occ:1.00 O C:GLY44 2.3 73.1 1.0 OG1 C:THR41 2.3 71.8 1.0 OE1 C:GLU55 2.4 64.2 1.0 OE2 C:GLU55 2.4 61.4 1.0 O C:THR41 2.4 69.2 1.0 OD2 C:ASP39 2.5 62.4 1.0 OD1 C:ASP39 2.6 69.5 1.0 O C:HOH701 2.7 63.7 1.0 CD C:GLU55 2.8 65.5 1.0 CG C:ASP39 2.8 65.9 1.0 CB C:THR41 3.4 74.6 1.0 C C:THR41 3.4 73.6 1.0 C C:GLY44 3.5 73.6 1.0 CA C:THR41 3.8 74.7 1.0 N C:THR41 4.1 73.6 1.0 OD2 C:ASP47 4.2 73.3 1.0 CG C:GLU55 4.3 63.2 1.0 CA C:GLY45 4.3 73.5 1.0 CB C:ASP39 4.4 66.8 1.0 N C:GLY45 4.4 77.0 1.0 N C:GLY44 4.4 77.5 1.0 OD1 C:ASN50 4.5 60.8 1.0 CA C:GLY44 4.6 74.7 1.0 N C:ILE42 4.6 70.4 1.0 CZ C:PHE49 4.7 58.9 1.0 NE2 C:HIS61 4.7 57.8 1.0 CG2 C:THR41 4.7 65.1 1.0 ND2 C:ASN50 4.9 58.2 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