Calcium in PDB 5s5d: Tubulin-Z32400357-Complex

The structure of Tubulin-Z32400357-Complex, PDB code: 5s5d 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)	63.42 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.07, 159.08, 179.22, 90, 90, 90
R / Rfree (%)	20 / 22.7

The structure of Tubulin-Z32400357-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z32400357-Complex (pdb code 5s5d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Tubulin-Z32400357-Complex, PDB code: 5s5d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Tubulin-Z32400357-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z32400357-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:70.8 occ:1.00 O A:GLY44 2.3 71.6 1.0 O A:THR41 2.4 72.4 1.0 O A:HOH654 2.4 56.9 1.0 OD2 A:ASP39 2.4 66.0 1.0 OE2 A:GLU55 2.4 58.8 1.0 OG1 A:THR41 2.4 69.5 1.0 OE1 A:GLU55 2.5 67.6 1.0 OD1 A:ASP39 2.6 68.7 1.0 CD A:GLU55 2.8 67.0 1.0 CG A:ASP39 2.8 69.8 1.0 CB A:THR41 3.3 74.4 1.0 C A:GLY44 3.4 72.0 1.0 C A:THR41 3.4 74.7 1.0 CA A:THR41 3.8 76.3 1.0 CA A:GLY45 4.1 76.7 1.0 N A:GLY45 4.1 75.9 1.0 N A:THR41 4.2 73.0 1.0 N A:GLY44 4.3 72.5 1.0 O A:HOH698 4.3 66.4 1.0 CG A:GLU55 4.3 61.8 1.0 CB A:ASP39 4.3 69.3 1.0 CA A:GLY44 4.4 72.4 1.0 N A:ILE42 4.6 72.0 1.0 CZ A:PHE49 4.6 65.5 1.0 OD1 A:ASN50 4.7 61.7 1.0 CG2 A:THR41 4.7 67.0 1.0 OD2 A:ASP47 4.8 62.2 1.0 NE2 A:HIS61 4.9 63.3 1.0 ND2 A:ASN50 4.9 58.0 1.0 O A:HOH753 5.0 67.1 1.0

Calcium binding site 2 out of 5 in the Tubulin-Z32400357-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z32400357-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:98.3 occ:1.00 O E:HOH203 2.5 70.0 1.0 O A:HOH674 3.3 48.1 1.0 O A:HOH745 3.4 54.4 1.0 OG A:SER158 3.6 51.3 1.0 NZ A:LYS166 3.9 45.5 1.0 OD2 E:ASP44 4.0 80.1 1.0 CB A:SER158 4.1 50.6 1.0 O A:GLY162 4.1 71.6 1.0 O A:HOH628 4.4 53.9 1.0 CA A:SER158 4.7 50.5 1.0 O A:GLU196 4.8 52.8 1.0 O A:HIS197 4.8 49.1 1.0 O A:LYS164 4.9 52.9 1.0 CA A:HIS197 5.0 48.6 1.0

Calcium binding site 3 out of 5 in the Tubulin-Z32400357-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z32400357-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:87.6 occ:1.00 OE1 B:GLU113 2.6 66.8 1.0 CD B:GLU113 3.5 64.0 1.0 OE2 B:GLU113 3.7 67.9 1.0 OE1 B:GLU110 4.3 43.4 1.0 CG B:GLU113 4.9 51.8 1.0

Calcium binding site 4 out of 5 in the Tubulin-Z32400357-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z32400357-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:47.0 occ:1.00 O C:GLY44 2.4 50.8 1.0 O C:THR41 2.4 50.0 1.0 OD2 C:ASP39 2.4 49.2 1.0 OE2 C:GLU55 2.4 43.6 1.0 OE1 C:GLU55 2.4 44.4 1.0 OD1 C:ASP39 2.5 50.3 1.0 OG1 C:THR41 2.5 52.3 1.0 O C:HOH627 2.5 41.8 1.0 CD C:GLU55 2.8 47.8 1.0 CG C:ASP39 2.8 49.2 1.0 C C:THR41 3.5 54.0 1.0 C C:GLY44 3.5 56.3 1.0 CB C:THR41 3.6 55.0 1.0 CA C:THR41 3.9 57.4 1.0 N C:THR41 4.2 55.3 1.0 CG C:GLU55 4.3 43.9 1.0 CB C:ASP39 4.3 48.3 1.0 CA C:GLY45 4.3 54.4 1.0 O C:HOH624 4.3 47.4 1.0 N C:GLY44 4.4 57.5 1.0 N C:GLY45 4.4 58.4 1.0 O C:HOH652 4.5 55.3 1.0 CA C:GLY44 4.5 57.8 1.0 NE2 C:HIS61 4.6 42.4 1.0 OD2 C:ASP47 4.6 47.3 1.0 N C:ILE42 4.6 52.5 1.0 CZ C:PHE49 4.7 46.6 1.0 OD1 C:ASN50 4.7 44.8 1.0 ND2 C:ASN50 4.9 41.9 1.0 CG2 C:THR41 4.9 50.4 1.0 CE1 C:PHE49 5.0 44.0 1.0

Calcium binding site 5 out of 5 in the Tubulin-Z32400357-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin-Z32400357-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:45.5 occ:1.00 O C:HOH857 2.2 47.2 1.0 OD1 C:ASP431 2.3 35.8 1.0 O C:HOH845 2.4 48.4 1.0 O C:HOH811 2.4 39.5 1.0 OE1 C:GLU434 2.5 48.8 1.0 O C:HOH813 2.8 52.6 1.0 OE2 C:GLU434 2.8 56.0 1.0 CD C:GLU434 3.0 53.1 1.0 CG C:ASP431 3.6 36.1 1.0 H11 C:NZJ505 3.8 51.0 1.0 O C:HOH706 4.1 40.1 1.0 OD2 C:ASP431 4.3 37.7 1.0 CA C:ASP431 4.3 37.6 1.0 CG C:GLU434 4.4 46.6 1.0 N C:ASP431 4.5 36.6 1.0 CB C:ASP431 4.5 33.9 1.0 O C:HOH893 4.6 43.5 1.0 H15 C:NZJ505 4.6 47.6 1.0 C11 C:NZJ505 4.7 42.5 1.0 O C:ALA427 4.7 35.2 1.0 CG C:LYS430 4.7 49.4 1.0 H5 C:NZJ505 4.8 47.6 1.0 CD C:LYS430 4.8 55.6 1.0 CE C:LYS430 4.8 63.6 1.0 O2 C:NZJ505 4.9 44.5 1.0 H6 C:NZJ505 4.9 45.4 1.0 C C:LYS430 4.9 39.0 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