Calcium in PDB 5s5r: Tubulin-Z33452106-Complex

The structure of Tubulin-Z33452106-Complex, PDB code: 5s5r 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)	72.81 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.24, 159.48, 178.6, 90, 90, 90
R / Rfree (%)	20.7 / 24.4

The structure of Tubulin-Z33452106-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z33452106-Complex (pdb code 5s5r). 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-Z33452106-Complex, PDB code: 5s5r:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z33452106-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z33452106-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:87.1 occ:1.00 O A:GLY44 2.3 94.1 1.0 O A:HOH631 2.3 86.6 1.0 OD1 A:ASP39 2.3 93.8 1.0 OD2 A:ASP39 2.3 88.5 1.0 OE2 A:GLU55 2.5 86.2 1.0 O A:THR41 2.5 94.2 1.0 OG1 A:THR41 2.5 91.8 1.0 OE1 A:GLU55 2.6 91.3 1.0 CG A:ASP39 2.7 88.9 1.0 CD A:GLU55 2.9 87.9 1.0 C A:GLY44 3.4 95.4 1.0 CB A:THR41 3.5 93.8 1.0 C A:THR41 3.5 97.9 1.0 CA A:THR41 3.9 99.9 1.0 CB A:ASP39 4.2 89.4 1.0 CA A:GLY45 4.2 101.9 1.0 N A:GLY45 4.2 98.7 1.0 CZ A:PHE49 4.2 80.9 1.0 N A:GLY44 4.2 94.2 1.0 N A:THR41 4.2 103.4 1.0 CG A:GLU55 4.4 82.8 1.0 CA A:GLY44 4.5 94.2 1.0 OD1 A:ASN50 4.5 88.4 1.0 OD2 A:ASP47 4.6 89.9 1.0 NE2 A:HIS61 4.7 84.7 1.0 N A:ILE42 4.7 94.5 1.0 CE1 A:PHE49 4.8 79.7 1.0 CG2 A:THR41 4.8 87.7 1.0 ND2 A:ASN50 4.9 83.1 1.0 CA A:ASP39 5.0 98.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z33452106-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z33452106-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:106.3 occ:1.00 O E:HOH201 2.7 92.2 1.0 O A:HOH663 3.2 80.5 1.0 O A:HOH608 3.3 68.1 1.0 OD2 E:ASP44 3.7 117.6 1.0 OG A:SER158 3.7 79.1 1.0 NZ A:LYS166 4.0 61.2 1.0 CB A:SER158 4.1 70.0 1.0 O A:GLY162 4.2 97.1 1.0 O A:GLU196 4.6 77.4 1.0 CA A:SER158 4.7 70.7 1.0 O A:HIS197 4.8 69.7 1.0 CG E:ASP44 4.9 118.3 1.0 CA A:HIS197 4.9 73.1 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z33452106-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z33452106-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:121.7 occ:1.00 OE1 B:GLU113 2.5 93.1 1.0 CD B:GLU113 3.3 90.0 1.0 OE2 B:GLU113 3.4 94.8 1.0 OE1 B:GLU110 4.6 66.4 1.0 CG B:GLU113 4.7 78.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z33452106-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z33452106-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:77.4 occ:1.00 OD1 C:ASP39 2.4 79.8 1.0 OD2 C:ASP39 2.4 72.9 1.0 OE2 C:GLU55 2.4 71.8 1.0 O C:THR41 2.4 79.3 1.0 OE1 C:GLU55 2.5 73.6 1.0 OG1 C:THR41 2.5 82.3 1.0 O C:GLY44 2.5 73.0 1.0 O C:HOH604 2.6 70.0 1.0 CG C:ASP39 2.7 75.0 1.0 CD C:GLU55 2.8 71.2 1.0 C C:THR41 3.4 85.9 1.0 CB C:THR41 3.5 87.1 1.0 C C:GLY44 3.7 77.2 1.0 CA C:THR41 3.8 84.6 1.0 N C:THR41 4.1 89.2 1.0 CB C:ASP39 4.2 77.6 1.0 CG C:GLU55 4.3 70.1 1.0 OD2 C:ASP47 4.3 81.0 1.0 CZ C:PHE49 4.4 63.7 1.0 CA C:GLY45 4.4 81.8 1.0 N C:GLY45 4.5 80.4 1.0 NE2 C:HIS61 4.6 65.2 1.0 N C:GLY44 4.6 79.8 1.0 N C:ILE42 4.6 81.7 1.0 OD1 C:ASN50 4.7 67.6 1.0 CA C:GLY44 4.8 80.8 1.0 CE1 C:PHE49 4.8 66.9 1.0 CG2 C:THR41 4.8 73.6 1.0 ND2 C:ASN50 4.9 63.1 1.0 O C:HOH713 4.9 69.6 1.0 CA C:ASP39 5.0 79.0 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