Calcium in PDB 5s5e: Tubulin-Z1515654336-Complex

The structure of Tubulin-Z1515654336-Complex, PDB code: 5s5e 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)	29.76 / 2.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.407, 159.503, 179.362, 90, 90, 90
R / Rfree (%)	18.7 / 22.7

The structure of Tubulin-Z1515654336-Complex also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Tubulin-Z1515654336-Complex (pdb code 5s5e). 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-Z1515654336-Complex, PDB code: 5s5e:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:83.9 occ:1.00 O A:GLY44 2.3 85.3 1.0 OE2 A:GLU55 2.4 88.1 1.0 OD2 A:ASP39 2.4 73.7 1.0 OD1 A:ASP39 2.4 85.4 1.0 OG1 A:THR41 2.5 89.0 1.0 O A:THR41 2.6 90.1 1.0 OE1 A:GLU55 2.8 89.3 1.0 CG A:ASP39 2.8 84.1 1.0 CD A:GLU55 2.9 87.8 1.0 C A:GLY44 3.4 87.6 1.0 CB A:THR41 3.5 87.4 1.0 C A:THR41 3.6 89.0 1.0 CA A:GLY45 4.0 94.2 1.0 CA A:THR41 4.0 89.6 1.0 N A:GLY45 4.1 89.1 1.0 N A:THR41 4.2 86.7 1.0 CB A:ASP39 4.3 84.3 1.0 N A:GLY44 4.3 92.5 1.0 OD2 A:ASP47 4.4 78.7 1.0 CZ A:PHE49 4.4 70.5 1.0 CG A:GLU55 4.4 82.9 1.0 CA A:GLY44 4.5 91.4 1.0 OD1 A:ASN50 4.6 81.0 1.0 N A:ILE42 4.8 91.3 1.0 CG2 A:THR41 4.8 88.2 1.0 CE1 A:PHE49 4.9 67.5 1.0 NE2 A:HIS61 4.9 78.5 1.0 ND2 A:ASN50 4.9 73.0 1.0 C A:GLY45 5.0 93.7 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:86.9 occ:1.00 O A:HOH651 3.2 67.1 1.0 O A:HOH628 3.4 58.9 1.0 OD2 E:ASP44 3.5 112.5 1.0 OG A:SER158 3.8 65.5 1.0 CB A:SER158 4.3 59.6 1.0 NZ A:LYS166 4.3 55.7 1.0 O A:GLU196 4.4 67.2 1.0 O A:GLY162 4.5 85.9 1.0 CG E:ASP44 4.7 112.1 1.0 CA A:HIS197 4.9 61.1 1.0 O A:HIS197 4.9 59.6 1.0 CA A:SER158 5.0 61.9 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:98.6 occ:1.00 OE1 B:GLU113 2.6 91.1 1.0 CD B:GLU113 3.5 88.1 1.0 OE2 B:GLU113 3.6 84.1 1.0 OE1 B:GLU110 4.6 54.7 1.0 CG B:GLU113 4.9 72.9 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:64.4 occ:1.00 OG1 C:THR41 2.4 70.2 1.0 O C:GLY44 2.4 71.1 1.0 O C:THR41 2.4 69.1 1.0 OE2 C:GLU55 2.4 59.4 1.0 OD2 C:ASP39 2.4 59.1 1.0 OE1 C:GLU55 2.4 61.3 1.0 O C:HOH601 2.5 58.4 1.0 OD1 C:ASP39 2.6 65.4 1.0 CD C:GLU55 2.7 57.8 1.0 CG C:ASP39 2.9 62.2 1.0 C C:THR41 3.4 69.5 1.0 CB C:THR41 3.4 67.8 1.0 C C:GLY44 3.6 71.2 1.0 CA C:THR41 3.8 67.1 1.0 N C:THR41 4.2 65.6 1.0 CG C:GLU55 4.3 55.9 1.0 CA C:GLY45 4.3 71.6 1.0 OD2 C:ASP47 4.4 69.4 1.0 CB C:ASP39 4.4 62.3 1.0 N C:GLY45 4.4 74.8 1.0 N C:ILE42 4.5 66.6 1.0 N C:GLY44 4.6 71.8 1.0 OD1 C:ASN50 4.6 57.9 1.0 CZ C:PHE49 4.6 53.4 1.0 CA C:GLY44 4.7 71.0 1.0 NE2 C:HIS61 4.7 51.8 1.0 CG2 C:THR41 4.7 54.8 1.0 O C:HOH716 4.8 59.4 1.0 ND2 C:ASN50 5.0 50.7 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