Calcium in PDB 5s64: Tubulin-Z28870646-Complex

The structure of Tubulin-Z28870646-Complex, PDB code: 5s64 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)	87.30 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.62, 158.42, 179.97, 90, 90, 90
R / Rfree (%)	21.4 / 26.2

The structure of Tubulin-Z28870646-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z28870646-Complex (pdb code 5s64). 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-Z28870646-Complex, PDB code: 5s64:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z28870646-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z28870646-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:122.1 occ:1.00 OE2 A:GLU55 2.3 118.3 1.0 OD2 A:ASP39 2.4 117.7 1.0 OD1 A:ASP39 2.4 122.5 1.0 OG1 A:THR41 2.4 126.9 1.0 O A:GLY44 2.4 140.5 1.0 CG A:ASP39 2.7 120.0 1.0 O A:THR41 2.8 126.6 1.0 OE1 A:GLU55 2.9 122.4 1.0 CD A:GLU55 2.9 118.5 1.0 CB A:THR41 3.5 128.0 1.0 C A:GLY44 3.6 140.0 1.0 C A:THR41 3.7 127.4 1.0 OD2 A:ASP47 4.0 112.8 1.0 CA A:THR41 4.0 126.0 1.0 CZ A:PHE49 4.1 100.3 1.0 CB A:ASP39 4.1 120.4 1.0 CA A:GLY45 4.1 136.8 1.0 N A:THR41 4.3 123.2 1.0 N A:GLY45 4.3 134.5 1.0 CG A:GLU55 4.4 115.1 1.0 OD1 A:ASN50 4.4 116.0 1.0 CE1 A:PHE49 4.4 100.7 1.0 NE2 A:HIS61 4.6 110.2 1.0 N A:GLY44 4.6 142.7 1.0 ND2 A:ASN50 4.6 104.6 1.0 CA A:GLY44 4.7 141.1 1.0 CG2 A:THR41 4.7 125.3 1.0 C A:GLY45 4.8 137.8 1.0 CA A:ASP39 4.9 126.9 1.0 CG A:ASN50 4.9 108.9 1.0 N A:ILE42 5.0 129.5 1.0 O A:GLY45 5.0 130.5 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z28870646-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z28870646-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:104.4 occ:1.00 NZ A:LYS166 3.8 99.1 1.0 OG A:SER158 3.8 94.1 1.0 OD2 E:ASP44 3.9 155.4 1.0 O A:GLY162 3.9 127.7 1.0 CB A:SER158 4.2 92.5 1.0 CE A:LYS166 4.5 86.6 1.0 O A:GLU196 4.8 97.3 1.0 CA A:SER158 4.8 97.0 1.0 CG E:ASP44 5.0 162.9 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z28870646-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z28870646-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:117.1 occ:1.00 OE1 B:GLU113 2.3 107.5 1.0 CD B:GLU113 3.2 106.8 1.0 OE2 B:GLU113 3.4 108.2 1.0 OE1 B:GLU110 4.4 90.2 1.0 CG B:GLU113 4.6 99.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z28870646-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z28870646-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:103.8 occ:1.00 OD2 C:ASP39 2.3 104.1 1.0 OE2 C:GLU55 2.3 101.1 1.0 O C:GLY44 2.3 104.0 1.0 O C:THR41 2.4 111.7 1.0 O C:HOH603 2.4 99.2 1.0 OD1 C:ASP39 2.5 107.6 1.0 OE1 C:GLU55 2.6 104.4 1.0 OG1 C:THR41 2.6 107.8 1.0 CG C:ASP39 2.7 105.6 1.0 CD C:GLU55 2.8 101.2 1.0 C C:THR41 3.4 114.3 1.0 CB C:THR41 3.5 108.5 1.0 C C:GLY44 3.6 107.2 1.0 CA C:THR41 3.8 114.7 1.0 N C:THR41 4.0 114.1 1.0 CB C:ASP39 4.2 108.6 1.0 CG C:GLU55 4.3 96.8 1.0 OD2 C:ASP47 4.3 100.0 1.0 CA C:GLY45 4.4 107.7 1.0 N C:GLY44 4.4 115.0 1.0 N C:GLY45 4.4 109.0 1.0 N C:ILE42 4.5 112.5 1.0 CA C:GLY44 4.5 112.3 1.0 OD1 C:ASN50 4.7 96.9 1.0 CZ C:PHE49 4.7 90.5 1.0 NE2 C:HIS61 4.8 100.0 1.0 CG2 C:THR41 4.9 103.1 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