Calcium in PDB 5s60: Tubulin-Z27695365-Complex

The structure of Tubulin-Z27695365-Complex, PDB code: 5s60 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)	63.73 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.35, 160.06, 178.51, 90, 90, 90
R / Rfree (%)	19.4 / 22.8

The structure of Tubulin-Z27695365-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z27695365-Complex (pdb code 5s60). 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-Z27695365-Complex, PDB code: 5s60:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z27695365-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z27695365-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:84.4 occ:1.00 O A:GLY44 2.3 86.8 1.0 OD2 A:ASP39 2.3 79.9 1.0 OD1 A:ASP39 2.4 87.1 1.0 O A:THR41 2.4 89.0 1.0 O A:HOH671 2.5 81.8 1.0 OE2 A:GLU55 2.5 79.2 1.0 OE1 A:GLU55 2.6 85.8 1.0 CG A:ASP39 2.7 82.2 1.0 OG1 A:THR41 2.7 85.6 1.0 CD A:GLU55 2.9 82.6 1.0 C A:THR41 3.5 92.0 1.0 C A:GLY44 3.5 92.7 1.0 CB A:THR41 3.5 90.5 1.0 CA A:THR41 3.9 95.1 1.0 N A:THR41 4.2 92.5 1.0 CB A:ASP39 4.2 83.7 1.0 N A:GLY44 4.2 94.5 1.0 CZ A:PHE49 4.2 76.0 1.0 CA A:GLY45 4.4 103.0 1.0 N A:GLY45 4.4 104.0 1.0 CG A:GLU55 4.4 76.4 1.0 CA A:GLY44 4.5 97.1 1.0 N A:ILE42 4.7 92.9 1.0 CE1 A:PHE49 4.7 74.1 1.0 NE2 A:HIS61 4.8 78.6 1.0 OD1 A:ASN50 4.8 83.1 1.0 ND2 A:ASN50 4.8 74.9 1.0 OD2 A:ASP47 4.9 79.0 1.0 CG2 A:THR41 4.9 82.9 1.0 N A:GLY43 5.0 91.9 1.0 CA A:ASP39 5.0 89.8 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z27695365-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z27695365-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:98.0 occ:1.00 OE2 B:GLU113 2.7 77.5 1.0 CD B:GLU113 3.7 75.3 1.0 O B:HOH633 3.8 66.3 1.0 OE1 B:GLU110 4.0 56.5 1.0 OE1 B:GLU113 4.0 77.6 1.0 CD B:GLU110 4.8 54.1 1.0 OE2 B:GLU110 4.8 62.1 1.0 O B:HOH693 4.9 63.3 1.0 OG B:SER97 5.0 74.5 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z27695365-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z27695365-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca604 b:59.8 occ:1.00 OG1 C:THR41 2.3 59.7 1.0 OD2 C:ASP39 2.4 54.7 1.0 O C:GLY44 2.4 60.9 1.0 OE1 C:GLU55 2.4 57.1 1.0 O C:HOH703 2.5 54.8 1.0 O C:THR41 2.5 61.9 1.0 OE2 C:GLU55 2.5 58.4 1.0 OD1 C:ASP39 2.6 63.4 1.0 CG C:ASP39 2.8 57.4 1.0 CD C:GLU55 2.8 57.2 1.0 CB C:THR41 3.5 71.6 1.0 C C:THR41 3.5 67.7 1.0 C C:GLY44 3.5 65.6 1.0 CA C:THR41 3.9 67.1 1.0 N C:THR41 4.1 64.3 1.0 OD2 C:ASP47 4.3 69.2 1.0 CA C:GLY45 4.3 67.6 1.0 CB C:ASP39 4.3 61.3 1.0 O C:HOH721 4.3 56.1 1.0 CG C:GLU55 4.3 55.4 1.0 N C:GLY45 4.3 70.0 1.0 N C:GLY44 4.4 64.5 1.0 CA C:GLY44 4.5 64.1 1.0 OD1 C:ASN50 4.6 58.4 1.0 CZ C:PHE49 4.6 55.5 1.0 N C:ILE42 4.7 64.7 1.0 NE2 C:HIS61 4.7 51.2 1.0 CG2 C:THR41 4.7 58.8 1.0 ND2 C:ASN50 4.8 49.5 1.0 CE1 C:PHE49 5.0 51.9 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z27695365-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z27695365-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:95.1 occ:1.00 O A:HOH608 2.7 80.4 1.0 O A:HOH655 3.1 62.5 1.0 O A:HOH697 3.1 69.5 1.0 OD2 E:ASP44 3.4 100.1 1.0 OG A:SER158 3.6 65.7 1.0 CB A:SER158 4.0 64.7 1.0 NZ A:LYS166 4.1 55.6 1.0 O A:GLU196 4.4 68.5 1.0 O A:GLY162 4.4 88.2 1.0 CG E:ASP44 4.5 100.1 1.0 O A:HOH611 4.5 62.7 1.0 CA A:SER158 4.8 62.2 1.0 CA A:HIS197 4.8 65.3 1.0 O A:HIS197 4.9 62.3 1.0 OD1 E:ASP44 4.9 94.6 1.0 ND1 A:HIS197 4.9 68.8 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