Calcium in PDB 5s4z: Tubulin-Z28290384-Complex

The structure of Tubulin-Z28290384-Complex, PDB code: 5s4z 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)	63.53 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.36, 159.26, 178.54, 90, 90, 90
R / Rfree (%)	20.5 / 24.2

The structure of Tubulin-Z28290384-Complex also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Fluorine	(F)	2 atoms

The binding sites of Calcium atom in the Tubulin-Z28290384-Complex (pdb code 5s4z). 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-Z28290384-Complex, PDB code: 5s4z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z28290384-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z28290384-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:70.8 occ:1.00 O A:GLY44 2.2 73.8 1.0 O A:HOH641 2.3 63.7 1.0 OD1 A:ASP39 2.4 76.4 1.0 OD2 A:ASP39 2.4 69.6 1.0 O A:THR41 2.5 80.5 1.0 OG1 A:THR41 2.5 72.1 1.0 OE2 A:GLU55 2.5 63.5 1.0 OE1 A:GLU55 2.6 71.9 1.0 CG A:ASP39 2.8 72.2 1.0 CD A:GLU55 2.9 69.7 1.0 C A:GLY44 3.4 79.3 1.0 CB A:THR41 3.4 77.4 1.0 C A:THR41 3.5 80.4 1.0 CA A:THR41 3.8 81.1 1.0 CA A:GLY45 4.1 81.2 1.0 N A:GLY45 4.1 80.6 1.0 N A:THR41 4.1 83.7 1.0 CB A:ASP39 4.3 74.7 1.0 N A:GLY44 4.3 78.0 1.0 CZ A:PHE49 4.4 64.6 1.0 CA A:GLY44 4.4 81.9 1.0 CG A:GLU55 4.4 67.9 1.0 OD1 A:ASN50 4.5 64.9 1.0 OD2 A:ASP47 4.6 66.3 1.0 N A:ILE42 4.7 83.8 1.0 CG2 A:THR41 4.7 70.6 1.0 O A:HOH703 4.8 74.2 1.0 CE1 A:PHE49 4.8 63.1 1.0 NE2 A:HIS61 4.9 70.7 1.0 ND2 A:ASN50 4.9 64.5 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z28290384-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z28290384-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:106.4 occ:1.00 OE1 B:GLU113 2.4 75.8 1.0 CD B:GLU113 3.4 73.8 1.0 OE2 B:GLU113 3.7 72.4 1.0 OE1 B:GLU110 3.9 49.7 1.0 CG B:GLU113 4.7 56.8 1.0 CD B:GLU110 4.8 53.5 1.0 OE2 B:GLU110 4.9 56.9 1.0 CB B:GLU113 4.9 51.4 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z28290384-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z28290384-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:54.0 occ:1.00 OG1 C:THR41 2.4 54.1 1.0 OE2 C:GLU55 2.4 50.4 1.0 OD2 C:ASP39 2.4 53.4 1.0 OE1 C:GLU55 2.5 49.3 1.0 OD1 C:ASP39 2.5 54.6 1.0 O C:GLY44 2.5 61.2 1.0 O C:HOH608 2.5 48.2 1.0 O C:THR41 2.5 52.9 1.0 CD C:GLU55 2.8 54.4 1.0 CG C:ASP39 2.8 52.3 1.0 CB C:THR41 3.5 63.7 1.0 C C:THR41 3.5 62.4 1.0 C C:GLY44 3.6 62.4 1.0 CA C:THR41 3.9 61.9 1.0 N C:THR41 4.2 61.5 1.0 OD2 C:ASP47 4.2 61.9 1.0 CG C:GLU55 4.3 50.0 1.0 CB C:ASP39 4.3 56.0 1.0 O C:HOH632 4.3 54.3 1.0 CA C:GLY45 4.3 63.6 1.0 N C:GLY45 4.4 65.6 1.0 N C:GLY44 4.4 65.5 1.0 O C:HOH643 4.4 51.1 1.0 CA C:GLY44 4.5 62.2 1.0 CZ C:PHE49 4.5 47.2 1.0 OD1 C:ASN50 4.6 49.0 1.0 N C:ILE42 4.7 60.1 1.0 NE2 C:HIS61 4.7 49.2 1.0 CG2 C:THR41 4.8 51.9 1.0 ND2 C:ASN50 4.9 41.4 1.0 CE1 C:PHE49 5.0 47.6 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z28290384-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z28290384-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:88.1 occ:1.00 O A:HOH697 3.1 63.8 1.0 OD2 E:ASP44 3.4 88.5 1.0 O A:HOH657 3.6 52.8 1.0 OG A:SER158 3.6 54.9 1.0 CB A:SER158 4.0 50.0 1.0 NZ A:LYS166 4.2 46.6 1.0 O A:GLY162 4.3 66.0 1.0 CG E:ASP44 4.6 87.7 1.0 O A:GLU196 4.6 52.4 1.0 CA A:SER158 4.7 53.0 1.0 O A:HOH604 4.7 53.7 1.0 CA A:HIS197 5.0 52.4 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