Calcium in PDB 5s5w: Tubulin-Z53860899-Complex

The structure of Tubulin-Z53860899-Complex, PDB code: 5s5w 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)	63.19 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.87, 158.35, 178.88, 90, 90, 90
R / Rfree (%)	22.4 / 26.5

The structure of Tubulin-Z53860899-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z53860899-Complex (pdb code 5s5w). 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-Z53860899-Complex, PDB code: 5s5w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z53860899-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z53860899-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:94.0 occ:1.00 O A:GLY44 2.3 92.0 1.0 OD2 A:ASP39 2.4 84.8 1.0 OE2 A:GLU55 2.4 87.9 1.0 OD1 A:ASP39 2.5 89.6 1.0 OG1 A:THR41 2.6 90.7 1.0 CG A:ASP39 2.8 87.8 1.0 OE1 A:GLU55 2.8 89.4 1.0 O A:THR41 2.8 92.7 1.0 CD A:GLU55 3.0 85.8 1.0 C A:GLY44 3.3 92.9 1.0 CB A:THR41 3.5 89.2 1.0 C A:THR41 3.8 94.0 1.0 CA A:GLY45 3.8 95.8 1.0 N A:GLY45 3.9 89.8 1.0 OD1 A:ASN50 4.1 82.9 1.0 CA A:THR41 4.1 97.8 1.0 CZ A:PHE49 4.2 77.2 1.0 OD2 A:ASP47 4.2 86.0 1.0 CB A:ASP39 4.2 85.8 1.0 N A:GLY44 4.3 95.9 1.0 CA A:GLY44 4.4 96.5 1.0 N A:THR41 4.4 97.2 1.0 CG A:GLU55 4.4 81.2 1.0 ND2 A:ASN50 4.7 77.8 1.0 C A:GLY45 4.7 96.6 1.0 CE1 A:PHE49 4.8 75.9 1.0 CG A:ASN50 4.8 81.3 1.0 CG2 A:THR41 4.8 84.8 1.0 NE2 A:HIS61 4.9 83.9 1.0 O A:GLY45 4.9 95.7 1.0 N A:ILE42 5.0 96.1 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z53860899-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z53860899-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:93.7 occ:1.00 O A:HOH603 2.4 78.9 1.0 O A:HOH636 3.3 65.4 1.0 OD2 E:ASP44 3.6 102.2 1.0 OG A:SER158 3.8 72.7 1.0 O A:HOH653 4.1 63.3 1.0 CB A:SER158 4.2 67.1 1.0 O A:GLY162 4.2 94.7 1.0 NZ A:LYS166 4.2 69.7 1.0 O A:GLU196 4.5 73.4 1.0 CG E:ASP44 4.6 103.9 1.0 O A:HIS197 4.7 67.5 1.0 CA A:SER158 4.8 67.2 1.0 CA A:HIS197 4.9 73.8 1.0 OD1 E:ASP44 5.0 98.3 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z53860899-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z53860899-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:104.1 occ:1.00 OE1 B:GLU113 2.7 78.0 1.0 CD B:GLU113 3.6 78.2 1.0 OE2 B:GLU113 3.9 78.7 1.0 OE1 B:GLU110 4.6 57.8 1.0 CG B:GLU113 5.0 64.4 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z53860899-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z53860899-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:71.3 occ:1.00 O C:GLY44 2.3 73.1 1.0 OG1 C:THR41 2.4 78.7 1.0 O C:THR41 2.5 71.8 1.0 OE2 C:GLU55 2.5 65.8 1.0 OE1 C:GLU55 2.5 72.2 1.0 OD1 C:ASP39 2.6 68.2 1.0 O C:HOH604 2.6 69.3 1.0 OD2 C:ASP39 2.7 64.6 1.0 CD C:GLU55 2.9 67.8 1.0 CG C:ASP39 3.0 71.8 1.0 CB C:THR41 3.3 75.9 1.0 C C:THR41 3.4 77.9 1.0 C C:GLY44 3.5 76.5 1.0 CA C:THR41 3.8 75.7 1.0 CA C:GLY45 4.1 80.2 1.0 N C:THR41 4.2 74.2 1.0 OD2 C:ASP47 4.2 78.9 1.0 N C:GLY45 4.3 82.0 1.0 CG C:GLU55 4.4 60.6 1.0 CB C:ASP39 4.5 73.2 1.0 N C:ILE42 4.5 79.1 1.0 OD1 C:ASN50 4.6 66.0 1.0 N C:GLY44 4.6 79.0 1.0 CG2 C:THR41 4.6 69.8 1.0 CZ C:PHE49 4.6 64.9 1.0 CA C:GLY44 4.7 79.5 1.0 ND2 C:ASN50 4.9 60.4 1.0 NE2 C:HIS61 4.9 63.6 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