Calcium in PDB 5s5b: Tubulin-Z906021418-Complex

The structure of Tubulin-Z906021418-Complex, PDB code: 5s5b 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)	63.37 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.02, 158.92, 179.41, 90, 90, 90
R / Rfree (%)	20.9 / 24.4

The structure of Tubulin-Z906021418-Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Tubulin-Z906021418-Complex (pdb code 5s5b). 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-Z906021418-Complex, PDB code: 5s5b:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z906021418-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:89.1 occ:1.00 O A:GLY44 2.2 91.9 1.0 OD1 A:ASP39 2.4 91.4 1.0 OE2 A:GLU55 2.5 90.6 1.0 OD2 A:ASP39 2.5 85.2 1.0 OG1 A:THR41 2.6 85.8 1.0 CG A:ASP39 2.8 89.9 1.0 O A:THR41 2.9 98.0 1.0 OE1 A:GLU55 3.0 91.9 1.0 CD A:GLU55 3.1 89.2 1.0 C A:GLY44 3.3 95.0 1.0 CB A:THR41 3.6 94.2 1.0 CA A:GLY45 3.8 95.9 1.0 C A:THR41 3.9 100.7 1.0 N A:GLY45 4.0 92.3 1.0 OD2 A:ASP47 4.0 87.3 1.0 OD1 A:ASN50 4.1 83.5 1.0 CZ A:PHE49 4.1 77.3 1.0 CA A:THR41 4.2 94.0 1.0 CB A:ASP39 4.3 90.9 1.0 N A:THR41 4.4 97.0 1.0 N A:GLY44 4.4 97.8 1.0 ND2 A:ASN50 4.4 82.8 1.0 CA A:GLY44 4.5 98.1 1.0 CG A:GLU55 4.6 87.3 1.0 C A:GLY45 4.6 94.3 1.0 CE1 A:PHE49 4.7 79.1 1.0 CG A:ASN50 4.7 82.4 1.0 NE2 A:HIS61 4.8 86.4 1.0 O A:GLY45 4.8 95.1 1.0 CG2 A:THR41 4.9 90.3 1.0 CG A:ASP47 5.0 86.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z906021418-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:101.3 occ:1.00 OE1 B:GLU113 2.7 77.4 1.0 CD B:GLU113 3.6 76.1 1.0 OE2 B:GLU113 3.7 75.4 1.0 OE1 B:GLU110 4.2 56.5 1.0 CG B:GLU113 5.0 66.0 1.0 CD B:GLU110 5.0 58.5 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z906021418-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:66.6 occ:1.00 O C:THR41 2.3 73.2 1.0 OE1 C:GLU55 2.4 65.2 1.0 O C:GLY44 2.4 71.8 1.0 OE2 C:GLU55 2.4 59.7 1.0 O C:HOH601 2.4 59.1 1.0 OG1 C:THR41 2.5 67.9 1.0 OD2 C:ASP39 2.5 59.2 1.0 OD1 C:ASP39 2.6 65.8 1.0 CD C:GLU55 2.7 65.2 1.0 CG C:ASP39 2.9 64.0 1.0 C C:THR41 3.3 73.9 1.0 CB C:THR41 3.4 74.5 1.0 C C:GLY44 3.5 73.5 1.0 CA C:THR41 3.8 73.0 1.0 N C:THR41 4.1 71.4 1.0 OD2 C:ASP47 4.2 73.7 1.0 CG C:GLU55 4.2 60.3 1.0 N C:GLY45 4.3 79.3 1.0 CA C:GLY45 4.3 76.4 1.0 N C:GLY44 4.4 78.1 1.0 CB C:ASP39 4.4 68.1 1.0 CA C:GLY44 4.5 75.2 1.0 N C:ILE42 4.5 78.2 1.0 CZ C:PHE49 4.6 56.6 1.0 OD1 C:ASN50 4.6 62.6 1.0 NE2 C:HIS61 4.6 58.6 1.0 CG2 C:THR41 4.8 64.7 1.0 ND2 C:ASN50 4.9 53.5 1.0 CA C:ILE42 5.0 78.5 1.0 CE1 C:PHE49 5.0 56.9 1.0 O C:HOH700 5.0 60.9 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z906021418-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:99.4 occ:1.00 O A:HOH652 3.0 75.3 1.0 OD2 E:ASP44 3.3 105.3 1.0 O A:HOH619 3.9 63.6 1.0 OG A:SER158 4.0 69.2 1.0 O A:GLU196 4.0 79.0 1.0 CB A:SER158 4.4 67.1 1.0 CG E:ASP44 4.4 104.7 1.0 NZ A:LYS166 4.6 64.9 1.0 CA A:HIS197 4.7 65.9 1.0 OD1 E:ASP44 4.7 99.1 1.0 O A:GLY162 4.8 86.1 1.0 O A:HIS197 4.9 67.5 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