Calcium in PDB 5s61: Tubulin-Z57472297-Complex

The structure of Tubulin-Z57472297-Complex, PDB code: 5s61 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)	62.59 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.36, 159.31, 178.35, 90, 90, 90
R / Rfree (%)	21.4 / 23.9

The structure of Tubulin-Z57472297-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z57472297-Complex (pdb code 5s61). 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-Z57472297-Complex, PDB code: 5s61:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z57472297-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z57472297-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:67.8 occ:1.00 O A:GLY44 2.3 71.4 1.0 O A:THR41 2.3 74.7 1.0 OD2 A:ASP39 2.3 69.4 1.0 OD1 A:ASP39 2.4 72.6 1.0 O A:HOH623 2.4 65.0 1.0 OE2 A:GLU55 2.5 63.5 1.0 OE1 A:GLU55 2.5 71.3 1.0 OG1 A:THR41 2.6 68.3 1.0 CG A:ASP39 2.7 67.7 1.0 CD A:GLU55 2.9 67.0 1.0 C A:THR41 3.4 76.7 1.0 CB A:THR41 3.4 75.5 1.0 C A:GLY44 3.5 75.9 1.0 CA A:THR41 3.8 77.7 1.0 N A:THR41 4.1 79.1 1.0 CB A:ASP39 4.2 68.5 1.0 CA A:GLY45 4.3 79.9 1.0 N A:GLY44 4.3 77.5 1.0 N A:GLY45 4.3 82.5 1.0 CG A:GLU55 4.4 63.3 1.0 CZ A:PHE49 4.4 62.9 1.0 CA A:GLY44 4.5 77.5 1.0 N A:ILE42 4.6 75.5 1.0 OD1 A:ASN50 4.6 66.7 1.0 NE2 A:HIS61 4.7 66.5 1.0 OD2 A:ASP47 4.7 69.2 1.0 CG2 A:THR41 4.8 68.1 1.0 CE1 A:PHE49 4.8 58.5 1.0 ND2 A:ASN50 4.9 62.9 1.0 CA A:ASP39 5.0 71.8 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z57472297-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z57472297-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:83.3 occ:1.00 O E:HOH201 2.5 64.7 1.0 O A:HOH674 3.2 54.3 1.0 O A:HOH627 3.4 51.1 1.0 OG A:SER158 3.8 51.1 1.0 OD2 E:ASP44 3.9 81.5 1.0 O A:HOH670 4.0 59.5 1.0 NZ A:LYS166 4.1 42.9 1.0 CB A:SER158 4.3 52.0 1.0 O A:GLY162 4.4 71.1 1.0 O A:GLU196 4.5 49.7 1.0 O A:HIS197 4.8 50.5 1.0 CA A:HIS197 4.9 46.6 1.0 CA A:SER158 4.9 50.8 1.0 CG E:ASP44 5.0 82.3 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z57472297-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z57472297-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:98.8 occ:1.00 OE1 B:GLU113 2.4 65.2 1.0 CD B:GLU113 3.3 60.9 1.0 OE2 B:GLU113 3.5 63.3 1.0 OE1 B:GLU110 4.7 45.9 1.0 CG B:GLU113 4.7 53.9 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z57472297-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z57472297-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:50.0 occ:1.00 OE1 C:GLU55 2.4 48.4 1.0 OE2 C:GLU55 2.4 47.0 1.0 O C:HOH602 2.4 45.8 1.0 OD2 C:ASP39 2.4 49.0 1.0 O C:THR41 2.5 53.5 1.0 O C:GLY44 2.5 59.3 1.0 OG1 C:THR41 2.5 50.2 1.0 OD1 C:ASP39 2.5 52.2 1.0 CD C:GLU55 2.7 50.3 1.0 CG C:ASP39 2.8 51.3 1.0 C C:THR41 3.5 57.8 1.0 C C:GLY44 3.5 59.9 1.0 CB C:THR41 3.6 56.2 1.0 CA C:THR41 4.0 59.1 1.0 CG C:GLU55 4.2 46.2 1.0 N C:THR41 4.2 59.1 1.0 OD2 C:ASP47 4.3 52.3 1.0 N C:GLY44 4.3 63.1 1.0 CB C:ASP39 4.3 52.0 1.0 N C:GLY45 4.4 57.8 1.0 CA C:GLY45 4.4 53.5 1.0 CA C:GLY44 4.5 62.1 1.0 CZ C:PHE49 4.5 46.4 1.0 NE2 C:HIS61 4.6 43.1 1.0 OD1 C:ASN50 4.6 48.0 1.0 N C:ILE42 4.6 55.5 1.0 CE1 C:PHE49 4.9 44.2 1.0 ND2 C:ASN50 4.9 42.0 1.0 CG2 C:THR41 4.9 51.8 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