Calcium in PDB 5s65: Tubulin-Z1354416068-Complex

The structure of Tubulin-Z1354416068-Complex, PDB code: 5s65 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)	62.70 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.19, 158.92, 179.34, 90, 90, 90
R / Rfree (%)	20.5 / 23.4

The structure of Tubulin-Z1354416068-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1354416068-Complex (pdb code 5s65). 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-Z1354416068-Complex, PDB code: 5s65:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1354416068-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1354416068-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:78.7 occ:1.00 O A:GLY44 2.2 75.6 1.0 O A:HOH620 2.3 75.1 1.0 OD2 A:ASP39 2.3 73.2 1.0 OD1 A:ASP39 2.5 80.9 1.0 OG1 A:THR41 2.5 77.0 1.0 O A:THR41 2.5 82.4 1.0 OE2 A:GLU55 2.5 70.7 1.0 CG A:ASP39 2.7 76.1 1.0 OE1 A:GLU55 2.8 75.6 1.0 CD A:GLU55 3.0 74.9 1.0 C A:GLY44 3.4 79.5 1.0 CB A:THR41 3.4 80.8 1.0 C A:THR41 3.5 85.2 1.0 CA A:THR41 3.9 86.7 1.0 CA A:GLY45 4.0 82.3 1.0 N A:THR41 4.1 89.3 1.0 N A:GLY45 4.1 77.1 1.0 CB A:ASP39 4.2 78.6 1.0 N A:GLY44 4.4 81.0 1.0 CZ A:PHE49 4.4 68.4 1.0 CA A:GLY44 4.5 80.0 1.0 OD2 A:ASP47 4.5 75.2 1.0 CG A:GLU55 4.5 71.7 1.0 OD1 A:ASN50 4.6 74.0 1.0 N A:ILE42 4.7 87.1 1.0 CG2 A:THR41 4.8 73.9 1.0 ND2 A:ASN50 4.8 70.2 1.0 NE2 A:HIS61 4.9 74.6 1.0 CE1 A:PHE49 4.9 67.4 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1354416068-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1354416068-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:87.4 occ:1.00 O E:HOH201 2.4 77.7 1.0 O A:HOH662 3.0 65.3 1.0 O A:HOH647 3.5 52.3 1.0 OD2 E:ASP44 3.7 95.7 1.0 OG A:SER158 3.8 58.5 1.0 CB A:SER158 4.2 56.1 1.0 O A:GLU196 4.2 64.1 1.0 NZ A:LYS166 4.3 51.1 1.0 O A:GLY162 4.6 74.3 1.0 CA A:HIS197 4.7 59.6 1.0 O A:HIS197 4.7 55.9 1.0 CG E:ASP44 4.8 94.4 1.0 CA A:SER158 4.9 56.0 1.0 C A:HIS197 5.0 60.5 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1354416068-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1354416068-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:93.2 occ:1.00 OE1 B:GLU113 2.6 76.6 1.0 CD B:GLU113 3.5 75.9 1.0 OE2 B:GLU113 3.7 78.5 1.0 OE1 B:GLU110 4.3 54.3 1.0 CG B:GLU113 4.9 68.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1354416068-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1354416068-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:52.8 occ:1.00 O C:GLY44 2.3 51.6 1.0 OE1 C:GLU55 2.4 48.8 1.0 O C:THR41 2.4 54.9 1.0 OG1 C:THR41 2.4 55.8 1.0 O C:HOH603 2.5 48.8 1.0 OE2 C:GLU55 2.5 47.5 1.0 OD2 C:ASP39 2.5 49.5 1.0 OD1 C:ASP39 2.6 53.3 1.0 CD C:GLU55 2.8 50.9 1.0 CG C:ASP39 2.9 52.9 1.0 C C:THR41 3.4 61.2 1.0 CB C:THR41 3.4 63.6 1.0 C C:GLY44 3.5 55.3 1.0 CA C:THR41 3.8 61.5 1.0 N C:THR41 4.1 57.7 1.0 O C:HOH615 4.2 60.0 1.0 N C:GLY44 4.3 53.9 1.0 CG C:GLU55 4.3 48.1 1.0 OD2 C:ASP47 4.3 57.2 1.0 CA C:GLY45 4.3 58.2 1.0 N C:GLY45 4.4 58.6 1.0 CB C:ASP39 4.4 55.0 1.0 CA C:GLY44 4.5 53.6 1.0 O C:HOH674 4.6 58.9 1.0 N C:ILE42 4.6 56.5 1.0 OD1 C:ASN50 4.6 51.2 1.0 CZ C:PHE49 4.7 49.2 1.0 NE2 C:HIS61 4.7 46.8 1.0 CG2 C:THR41 4.8 55.1 1.0 ND2 C:ASN50 4.9 43.5 1.0 CE1 C:PHE49 4.9 47.5 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