Calcium in PDB 5s52: Tubulin-Z50145861-Complex

The structure of Tubulin-Z50145861-Complex, PDB code: 5s52 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)	118.67 / 2.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.09, 161.57, 174.88, 90, 90, 90
R / Rfree (%)	23.8 / 29.7

The structure of Tubulin-Z50145861-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z50145861-Complex (pdb code 5s52). 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-Z50145861-Complex, PDB code: 5s52:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z50145861-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z50145861-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:102.7 occ:1.00 OE2 A:GLU55 2.3 100.3 1.0 OG1 A:THR41 2.3 118.7 1.0 O A:GLY44 2.4 122.7 1.0 O A:THR41 2.7 109.9 1.0 OE1 A:GLU55 2.7 106.9 1.0 OD1 A:ASP39 2.8 106.8 1.0 CD A:GLU55 2.9 103.1 1.0 OD2 A:ASP39 2.9 105.3 1.0 CG A:ASP39 3.2 103.1 1.0 CB A:THR41 3.4 115.3 1.0 C A:GLY44 3.6 125.2 1.0 C A:THR41 3.6 110.5 1.0 CA A:THR41 4.0 111.5 1.0 OD2 A:ASP47 4.0 116.1 1.0 CA A:GLY45 4.2 129.8 1.0 OD1 A:ASN50 4.3 102.9 1.0 N A:GLY45 4.3 132.6 1.0 CG A:GLU55 4.4 99.1 1.0 N A:THR41 4.4 118.0 1.0 CZ A:PHE49 4.5 90.8 1.0 ND2 A:ASN50 4.5 94.6 1.0 N A:GLY44 4.6 126.4 1.0 CA A:GLY44 4.6 124.2 1.0 CG2 A:THR41 4.6 107.6 1.0 CB A:ASP39 4.7 96.7 1.0 N A:ILE42 4.8 110.3 1.0 CG A:ASN50 4.8 99.2 1.0 C A:GLY45 4.9 126.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z50145861-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z50145861-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:99.6 occ:1.00 O E:HOH203 3.1 104.7 1.0 NZ A:LYS166 3.8 88.9 1.0 OG A:SER158 3.8 83.0 1.0 O A:GLY162 4.1 116.0 1.0 OD1 A:ASP199 4.3 82.4 1.0 CB A:SER158 4.3 78.8 1.0 O A:HIS197 4.4 77.9 1.0 O A:GLU196 4.7 97.7 1.0 O A:LYS164 4.7 94.1 1.0 CA A:HIS197 4.7 78.9 1.0 C A:HIS197 4.9 78.1 1.0 CA A:SER158 4.9 80.7 1.0 OD2 A:ASP199 5.0 78.2 1.0 CE A:LYS166 5.0 82.5 1.0 OD2 E:ASP44 5.0 179.7 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z50145861-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z50145861-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:112.4 occ:1.00 OE1 B:GLU113 2.5 101.6 1.0 CD B:GLU113 3.2 106.6 1.0 OE2 B:GLU113 3.2 110.6 1.0 OE1 B:GLU110 3.9 70.7 1.0 CG B:GLU113 4.6 98.4 1.0 CD B:GLU110 5.0 71.7 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z50145861-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z50145861-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:73.2 occ:1.00 O C:HOH603 2.4 66.4 1.0 OE2 C:GLU55 2.4 76.5 1.0 OG1 C:THR41 2.4 80.4 1.0 O C:GLY44 2.5 91.0 1.0 O C:THR41 2.6 86.4 1.0 OD1 C:ASP39 2.7 80.7 1.0 OD2 C:ASP39 2.7 70.1 1.0 OE1 C:GLU55 2.7 81.8 1.0 CG C:ASP39 2.9 81.0 1.0 CD C:GLU55 2.9 75.5 1.0 C C:THR41 3.6 87.7 1.0 C C:GLY44 3.6 90.8 1.0 CB C:THR41 3.7 83.7 1.0 CA C:THR41 4.0 86.1 1.0 N C:THR41 4.2 92.0 1.0 CB C:ASP39 4.3 90.7 1.0 CA C:GLY45 4.4 77.7 1.0 OD1 C:ASN50 4.4 75.4 1.0 CG C:GLU55 4.4 71.4 1.0 N C:GLY45 4.4 86.6 1.0 N C:GLY44 4.5 89.2 1.0 OD2 C:ASP47 4.5 67.6 1.0 CZ C:PHE49 4.5 63.9 1.0 CA C:GLY44 4.6 87.7 1.0 NE2 C:HIS61 4.7 69.6 1.0 N C:ILE42 4.8 88.3 1.0 CG2 C:THR41 4.8 87.2 1.0 CE1 C:PHE49 5.0 58.6 1.0 ND2 C:ASN50 5.0 62.7 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