Calcium in PDB 5s5l: Tubulin-Z1492796719-Complex

The structure of Tubulin-Z1492796719-Complex, PDB code: 5s5l 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)	62.67 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.12, 159.02, 179.19, 90, 90, 90
R / Rfree (%)	20.4 / 23.5

The structure of Tubulin-Z1492796719-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1492796719-Complex (pdb code 5s5l). 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-Z1492796719-Complex, PDB code: 5s5l:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1492796719-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:79.5 occ:1.00 O A:GLY44 2.2 86.8 1.0 OE2 A:GLU55 2.3 78.4 1.0 OD2 A:ASP39 2.4 80.5 1.0 O A:HOH624 2.4 79.3 1.0 OD1 A:ASP39 2.5 84.6 1.0 O A:THR41 2.5 90.1 1.0 OG1 A:THR41 2.6 77.3 1.0 OE1 A:GLU55 2.7 83.4 1.0 CG A:ASP39 2.8 80.6 1.0 CD A:GLU55 2.8 81.2 1.0 C A:GLY44 3.2 86.1 1.0 CB A:THR41 3.5 88.5 1.0 C A:THR41 3.6 87.5 1.0 CA A:GLY45 3.9 91.5 1.0 N A:GLY45 3.9 88.2 1.0 CA A:THR41 4.0 92.1 1.0 N A:GLY44 4.2 87.2 1.0 CA A:GLY44 4.3 86.8 1.0 CB A:ASP39 4.3 82.8 1.0 N A:THR41 4.3 90.6 1.0 CG A:GLU55 4.3 79.8 1.0 CZ A:PHE49 4.5 75.5 1.0 OD1 A:ASN50 4.5 81.2 1.0 ND2 A:ASN50 4.7 75.3 1.0 OD2 A:ASP47 4.7 82.2 1.0 N A:ILE42 4.8 88.7 1.0 C A:GLY45 4.8 91.6 1.0 CG2 A:THR41 4.9 77.4 1.0 NE2 A:HIS61 4.9 78.8 1.0 CE1 A:PHE49 5.0 72.7 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1492796719-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:93.3 occ:1.00 O A:HOH665 3.2 69.1 1.0 O A:HOH614 3.4 61.3 1.0 OD2 E:ASP44 3.5 100.4 1.0 OG A:SER158 3.6 66.3 1.0 O A:HOH611 3.7 77.1 1.0 CB A:SER158 3.9 65.4 1.0 NZ A:LYS166 4.0 66.2 1.0 O A:GLY162 4.1 90.4 1.0 CA A:SER158 4.5 65.4 1.0 O A:GLU196 4.6 70.1 1.0 CG E:ASP44 4.7 102.3 1.0 CA A:HIS197 4.9 65.1 1.0 O A:HIS197 5.0 65.3 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1492796719-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:109.5 occ:1.00 OE1 B:GLU113 2.5 80.3 1.0 CD B:GLU113 3.4 76.6 1.0 OE2 B:GLU113 3.7 80.2 1.0 OE1 B:GLU110 4.7 48.4 1.0 CG B:GLU113 4.8 68.7 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1492796719-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:61.6 occ:1.00 O C:GLY44 2.4 62.0 1.0 OD2 C:ASP39 2.4 56.8 1.0 OE1 C:GLU55 2.4 60.3 1.0 OE2 C:GLU55 2.4 57.2 1.0 OG1 C:THR41 2.4 65.9 1.0 O C:THR41 2.4 65.4 1.0 OD1 C:ASP39 2.6 61.3 1.0 O C:HOH601 2.6 55.0 1.0 CD C:GLU55 2.8 59.5 1.0 CG C:ASP39 2.8 58.3 1.0 CB C:THR41 3.4 71.2 1.0 C C:THR41 3.4 70.6 1.0 C C:GLY44 3.6 68.2 1.0 CA C:THR41 3.9 66.1 1.0 N C:THR41 4.2 69.4 1.0 OD2 C:ASP47 4.2 68.1 1.0 CG C:GLU55 4.3 58.6 1.0 CB C:ASP39 4.3 62.6 1.0 CA C:GLY45 4.3 68.5 1.0 N C:GLY45 4.4 71.6 1.0 N C:GLY44 4.4 67.9 1.0 CZ C:PHE49 4.6 54.8 1.0 NE2 C:HIS61 4.6 53.6 1.0 CA C:GLY44 4.6 69.5 1.0 N C:ILE42 4.6 68.1 1.0 OD1 C:ASN50 4.6 57.7 1.0 CG2 C:THR41 4.8 58.9 1.0 ND2 C:ASN50 4.9 52.4 1.0 O C:HOH743 4.9 59.8 1.0 CE1 C:PHE49 4.9 51.9 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