Calcium in PDB 5s4v: Tubulin-Z57040482-Complex

The structure of Tubulin-Z57040482-Complex, PDB code: 5s4v 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)	63.02 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.42, 158.06, 178.36, 90, 90, 90
R / Rfree (%)	20.5 / 24.2

The structure of Tubulin-Z57040482-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z57040482-Complex (pdb code 5s4v). 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-Z57040482-Complex, PDB code: 5s4v:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z57040482-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z57040482-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:87.6 occ:1.00 OD1 A:ASP39 2.3 88.0 1.0 OD2 A:ASP39 2.3 80.7 1.0 O A:GLY44 2.3 88.2 1.0 OE2 A:GLU55 2.4 82.3 1.0 O A:HOH604 2.5 84.1 1.0 O A:THR41 2.6 91.3 1.0 OG1 A:THR41 2.6 83.8 1.0 OE1 A:GLU55 2.6 85.2 1.0 CG A:ASP39 2.6 85.2 1.0 CD A:GLU55 2.8 88.5 1.0 C A:GLY44 3.5 92.9 1.0 CB A:THR41 3.6 91.1 1.0 C A:THR41 3.6 93.0 1.0 CA A:THR41 4.0 95.7 1.0 CB A:ASP39 4.1 84.6 1.0 N A:THR41 4.2 96.0 1.0 CZ A:PHE49 4.2 77.7 1.0 N A:GLY44 4.3 92.8 1.0 CA A:GLY45 4.3 100.9 1.0 CG A:GLU55 4.3 80.4 1.0 N A:GLY45 4.3 99.1 1.0 OD2 A:ASP47 4.5 86.0 1.0 OD1 A:ASN50 4.5 87.8 1.0 CA A:GLY44 4.5 91.6 1.0 NE2 A:HIS61 4.7 80.5 1.0 N A:ILE42 4.8 91.7 1.0 ND2 A:ASN50 4.9 83.1 1.0 CG2 A:THR41 4.9 84.5 1.0 CA A:ASP39 4.9 86.0 1.0 CE1 A:PHE49 5.0 76.7 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z57040482-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z57040482-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:97.3 occ:1.00 O A:HOH661 2.4 76.0 1.0 O A:HOH660 2.5 78.2 1.0 OD2 E:ASP44 3.5 95.0 1.0 O A:GLU196 3.6 75.2 1.0 OG A:SER158 3.8 76.8 1.0 O A:HOH609 4.0 65.0 1.0 CA A:HIS197 4.3 67.6 1.0 NZ A:LYS166 4.4 62.9 1.0 CB A:SER158 4.4 66.2 1.0 CG E:ASP44 4.4 98.4 1.0 OD1 E:ASP44 4.5 97.7 1.0 O A:HIS197 4.5 66.7 1.0 C A:GLU196 4.7 70.6 1.0 C A:HIS197 4.7 67.5 1.0 ND1 A:HIS197 4.8 74.9 1.0 OD1 A:ASP199 5.0 82.8 1.0 N A:HIS197 5.0 65.1 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z57040482-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z57040482-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:106.6 occ:1.00 OE1 B:GLU113 2.5 79.7 1.0 OE2 B:GLU113 3.0 90.3 1.0 CD B:GLU113 3.1 84.6 1.0 CG B:GLU113 4.5 72.5 1.0 OE1 B:GLU110 4.9 60.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z57040482-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z57040482-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:74.4 occ:1.00 OD2 C:ASP39 2.3 70.4 1.0 O C:GLY44 2.3 73.3 1.0 OE1 C:GLU55 2.4 69.6 1.0 O C:THR41 2.4 76.4 1.0 OG1 C:THR41 2.5 80.5 1.0 OD1 C:ASP39 2.5 75.9 1.0 OE2 C:GLU55 2.5 68.2 1.0 O C:HOH605 2.5 65.2 1.0 CG C:ASP39 2.7 70.8 1.0 CD C:GLU55 2.8 67.6 1.0 C C:THR41 3.4 77.5 1.0 CB C:THR41 3.5 82.3 1.0 C C:GLY44 3.6 75.5 1.0 CA C:THR41 3.9 77.3 1.0 N C:THR41 4.2 80.2 1.0 CB C:ASP39 4.2 76.5 1.0 CG C:GLU55 4.3 67.0 1.0 OD2 C:ASP47 4.3 76.9 1.0 N C:GLY44 4.4 76.5 1.0 CA C:GLY45 4.4 82.1 1.0 N C:GLY45 4.4 80.8 1.0 CZ C:PHE49 4.5 59.2 1.0 CA C:GLY44 4.6 75.4 1.0 NE2 C:HIS61 4.6 62.8 1.0 OD1 C:ASN50 4.6 67.4 1.0 N C:ILE42 4.6 80.5 1.0 CG2 C:THR41 4.8 72.4 1.0 ND2 C:ASN50 4.9 61.1 1.0 CE1 C:PHE49 4.9 63.6 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