Calcium in PDB 5s5h: Tubulin-Z2074076908-Complex

The structure of Tubulin-Z2074076908-Complex, PDB code: 5s5h 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)	90.54 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.91, 158.89, 179.24, 90, 90, 90
R / Rfree (%)	21.6 / 27

The structure of Tubulin-Z2074076908-Complex also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Tubulin-Z2074076908-Complex (pdb code 5s5h). 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-Z2074076908-Complex, PDB code: 5s5h:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2074076908-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2074076908-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:109.0 occ:1.00 OE2 A:GLU55 2.3 111.0 1.0 O A:GLY44 2.3 115.9 1.0 OD1 A:ASP39 2.4 112.5 1.0 OD2 A:ASP39 2.5 108.5 1.0 OG1 A:THR41 2.6 113.3 1.0 O A:THR41 2.7 116.1 1.0 CG A:ASP39 2.8 111.2 1.0 CD A:GLU55 3.0 111.4 1.0 OE1 A:GLU55 3.0 114.4 1.0 C A:GLY44 3.4 119.1 1.0 CB A:THR41 3.7 113.9 1.0 C A:THR41 3.7 116.3 1.0 CA A:GLY45 3.9 127.3 1.0 OD2 A:ASP47 4.0 103.6 1.0 CZ A:PHE49 4.0 100.5 1.0 OD1 A:ASN50 4.1 110.8 1.0 N A:GLY45 4.1 123.9 1.0 CA A:THR41 4.2 117.2 1.0 CB A:ASP39 4.2 113.9 1.0 N A:THR41 4.4 115.8 1.0 CG A:GLU55 4.5 108.3 1.0 N A:GLY44 4.5 122.3 1.0 CA A:GLY44 4.6 120.3 1.0 ND2 A:ASN50 4.6 97.7 1.0 C A:GLY45 4.7 127.5 1.0 CG A:ASN50 4.8 109.5 1.0 CE2 A:PHE49 4.8 98.2 1.0 CE1 A:PHE49 4.8 98.4 1.0 N A:ILE42 4.9 116.3 1.0 CG2 A:THR41 4.9 108.7 1.0 O A:GLY45 4.9 125.4 1.0 NE2 A:HIS61 5.0 106.3 1.0 CA A:ASP39 5.0 117.3 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2074076908-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2074076908-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:106.0 occ:1.00 O A:HOH612 2.7 106.7 1.0 O A:HOH611 3.5 79.7 1.0 OD2 E:ASP44 3.6 137.3 1.0 OG A:SER158 3.8 93.6 1.0 O A:GLU196 4.0 98.6 1.0 CB A:SER158 4.3 90.2 1.0 CG E:ASP44 4.4 136.2 1.0 OD1 E:ASP44 4.4 131.9 1.0 NZ A:LYS166 4.5 85.8 1.0 CA A:HIS197 4.5 89.9 1.0 O A:HIS197 4.7 89.3 1.0 ND1 A:HIS197 4.7 100.5 1.0 O A:GLY162 4.9 117.2 1.0 C A:HIS197 4.9 90.9 1.0 OD1 A:ASP199 4.9 100.0 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2074076908-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2074076908-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:116.5 occ:1.00 OE1 B:GLU113 2.6 105.0 1.0 OE2 B:GLU113 3.3 98.3 1.0 CD B:GLU113 3.3 101.7 1.0 CG B:GLU113 4.8 86.8 1.0 OE1 B:GLU110 4.8 78.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2074076908-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2074076908-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:84.8 occ:1.00 O C:THR41 2.3 90.6 1.0 OD2 C:ASP39 2.4 82.3 1.0 O C:GLY44 2.4 84.9 1.0 OG1 C:THR41 2.4 92.6 1.0 OD1 C:ASP39 2.4 82.8 1.0 OE1 C:GLU55 2.5 87.2 1.0 O C:HOH602 2.7 81.3 1.0 OE2 C:GLU55 2.7 82.0 1.0 CG C:ASP39 2.7 82.5 1.0 CD C:GLU55 2.9 81.8 1.0 CB C:THR41 3.3 92.7 1.0 C C:THR41 3.3 91.9 1.0 C C:GLY44 3.6 90.4 1.0 CA C:THR41 3.7 89.1 1.0 N C:THR41 4.0 86.2 1.0 CB C:ASP39 4.2 84.2 1.0 CA C:GLY45 4.3 93.3 1.0 N C:GLY45 4.4 94.8 1.0 OD2 C:ASP47 4.4 90.3 1.0 CG C:GLU55 4.5 79.0 1.0 N C:GLY44 4.5 97.5 1.0 N C:ILE42 4.5 92.3 1.0 CA C:GLY44 4.6 93.3 1.0 OD1 C:ASN50 4.6 81.2 1.0 CG2 C:THR41 4.7 79.9 1.0 CZ C:PHE49 4.8 69.0 1.0 NE2 C:HIS61 4.9 76.4 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