Calcium in PDB 5s55: Tubulin-Z106307058-Complex

The structure of Tubulin-Z106307058-Complex, PDB code: 5s55 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)	62.68 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.64, 158.15, 180.17, 90, 90, 90
R / Rfree (%)	20.6 / 23.6

The structure of Tubulin-Z106307058-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z106307058-Complex (pdb code 5s55). 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-Z106307058-Complex, PDB code: 5s55:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z106307058-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z106307058-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:86.1 occ:1.00 O A:GLY44 2.3 91.1 1.0 OE2 A:GLU55 2.4 85.5 1.0 OG1 A:THR41 2.4 90.7 1.0 OD1 A:ASP39 2.4 90.8 1.0 OD2 A:ASP39 2.5 87.3 1.0 O A:THR41 2.6 95.3 1.0 CG A:ASP39 2.8 87.3 1.0 OE1 A:GLU55 2.9 89.1 1.0 CD A:GLU55 3.0 87.3 1.0 C A:GLY44 3.4 95.2 1.0 CB A:THR41 3.4 92.4 1.0 C A:THR41 3.6 96.4 1.0 CA A:GLY45 3.9 97.5 1.0 CA A:THR41 4.0 97.1 1.0 N A:GLY45 4.1 94.8 1.0 OD2 A:ASP47 4.1 82.7 1.0 CZ A:PHE49 4.2 76.7 1.0 OD1 A:ASN50 4.2 84.1 1.0 CB A:ASP39 4.3 88.5 1.0 N A:THR41 4.3 97.8 1.0 CG A:GLU55 4.5 84.6 1.0 CA A:GLY44 4.6 95.4 1.0 N A:GLY44 4.6 95.5 1.0 ND2 A:ASN50 4.6 76.2 1.0 CG2 A:THR41 4.7 85.1 1.0 C A:GLY45 4.7 95.6 1.0 N A:ILE42 4.8 102.0 1.0 NE2 A:HIS61 4.9 82.9 1.0 CG A:ASN50 4.9 78.3 1.0 CE1 A:PHE49 4.9 71.8 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z106307058-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z106307058-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:90.9 occ:1.00 O A:HOH656 2.5 69.6 1.0 O A:HOH639 2.5 69.8 1.0 O E:HOH204 2.6 74.6 1.0 O A:HOH636 3.5 60.5 1.0 O A:HOH635 3.6 71.1 1.0 OD2 E:ASP44 3.9 78.2 1.0 O A:GLU196 4.0 67.0 1.0 OG A:SER158 4.1 62.6 1.0 OD1 A:ASP199 4.5 62.3 1.0 CA A:HIS197 4.5 62.3 1.0 O A:HIS197 4.5 61.2 1.0 NZ A:LYS166 4.6 61.3 1.0 CB A:SER158 4.8 63.8 1.0 C A:HIS197 4.8 63.0 1.0 O A:GLY162 4.9 87.5 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z106307058-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z106307058-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:101.0 occ:1.00 OE1 B:GLU113 2.6 72.2 1.0 CD B:GLU113 3.4 74.5 1.0 OE2 B:GLU113 3.5 75.0 1.0 OE1 B:GLU110 4.5 54.0 1.0 CG B:GLU113 4.9 64.3 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z106307058-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z106307058-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:68.4 occ:1.00 OE1 C:GLU55 2.4 65.5 1.0 OE2 C:GLU55 2.4 61.4 1.0 OD2 C:ASP39 2.4 66.9 1.0 O C:THR41 2.4 77.0 1.0 O C:GLY44 2.4 79.7 1.0 OG1 C:THR41 2.5 71.4 1.0 OD1 C:ASP39 2.6 71.8 1.0 O C:HOH606 2.7 62.2 1.0 CD C:GLU55 2.7 64.8 1.0 CG C:ASP39 2.8 67.8 1.0 C C:THR41 3.4 78.6 1.0 CB C:THR41 3.5 72.3 1.0 C C:GLY44 3.6 78.3 1.0 CA C:THR41 3.9 76.6 1.0 N C:THR41 4.2 77.5 1.0 CG C:GLU55 4.2 59.8 1.0 CB C:ASP39 4.3 69.1 1.0 CA C:GLY45 4.4 82.6 1.0 OD2 C:ASP47 4.4 71.9 1.0 N C:GLY45 4.4 80.5 1.0 N C:GLY44 4.5 79.7 1.0 NE2 C:HIS61 4.6 57.2 1.0 N C:ILE42 4.6 76.6 1.0 CA C:GLY44 4.6 78.7 1.0 OD1 C:ASN50 4.7 62.8 1.0 CZ C:PHE49 4.7 57.7 1.0 CG2 C:THR41 4.8 64.4 1.0 O C:HOH762 4.9 68.0 1.0 ND2 C:ASN50 5.0 54.8 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