Calcium in PDB 5s5m: Tubulin-Z45527714-Complex

The structure of Tubulin-Z45527714-Complex, PDB code: 5s5m 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)	55.92 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.66, 159.8, 179.1, 90, 90, 90
R / Rfree (%)	21.5 / 26.9

The structure of Tubulin-Z45527714-Complex also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Tubulin-Z45527714-Complex (pdb code 5s5m). 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-Z45527714-Complex, PDB code: 5s5m:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z45527714-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:124.8 occ:1.00 O A:GLY44 2.3 137.1 1.0 OE2 A:GLU55 2.3 122.0 1.0 OG1 A:THR41 2.4 128.8 1.0 OD2 A:ASP39 2.6 115.9 1.0 O A:THR41 2.7 127.5 1.0 OD1 A:ASP39 2.8 121.0 1.0 OE1 A:GLU55 2.9 123.8 1.0 CD A:GLU55 2.9 121.4 1.0 CG A:ASP39 3.1 119.8 1.0 CB A:THR41 3.4 125.5 1.0 C A:GLY44 3.4 138.4 1.0 C A:THR41 3.6 131.5 1.0 OD2 A:ASP47 3.9 116.0 1.0 CA A:THR41 4.0 127.9 1.0 CA A:GLY45 4.0 156.8 1.0 N A:GLY45 4.2 154.5 1.0 OD1 A:ASN50 4.2 125.0 1.0 CZ A:PHE49 4.2 103.2 1.0 N A:THR41 4.3 127.2 1.0 N A:GLY44 4.4 137.6 1.0 CG A:GLU55 4.4 115.8 1.0 CA A:GLY44 4.5 139.1 1.0 CB A:ASP39 4.6 121.2 1.0 C A:GLY45 4.7 157.9 1.0 CG2 A:THR41 4.7 114.0 1.0 ND2 A:ASN50 4.7 111.1 1.0 CE1 A:PHE49 4.7 104.3 1.0 O A:GLY45 4.8 154.6 1.0 N A:ILE42 4.8 129.8 1.0 CG A:ASN50 4.9 116.6 1.0 CG A:ASP47 4.9 119.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z45527714-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:111.6 occ:1.00 O A:HOH608 2.8 101.7 1.0 OD2 E:ASP44 3.7 131.7 1.0 NZ A:LYS166 4.1 92.7 1.0 OG A:SER158 4.1 93.4 1.0 O A:GLU196 4.2 101.9 1.0 CB A:SER158 4.4 90.0 1.0 O A:GLY162 4.6 133.2 1.0 CA A:HIS197 4.7 98.2 1.0 CG E:ASP44 4.7 130.8 1.0 O A:HIS197 4.8 95.3 1.0 C A:HIS197 5.0 96.5 1.0 OD1 E:ASP44 5.0 128.8 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z45527714-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:140.6 occ:1.00 OE1 B:GLU113 2.9 105.4 1.0 CD B:GLU113 3.8 105.7 1.0 OE2 B:GLU113 3.8 108.5 1.0 OE1 B:GLU110 4.3 93.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z45527714-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:100.5 occ:1.00 OD2 C:ASP39 2.3 98.9 1.0 OE2 C:GLU55 2.3 94.4 1.0 O C:THR41 2.3 103.0 1.0 OE1 C:GLU55 2.4 102.1 1.0 OG1 C:THR41 2.4 108.3 1.0 O C:GLY44 2.5 105.8 1.0 OD1 C:ASP39 2.5 99.5 1.0 CD C:GLU55 2.7 93.8 1.0 CG C:ASP39 2.7 101.4 1.0 C C:THR41 3.4 106.0 1.0 CB C:THR41 3.4 108.4 1.0 C C:GLY44 3.6 107.0 1.0 CA C:THR41 3.8 109.7 1.0 OD2 C:ASP47 4.0 102.0 1.0 N C:THR41 4.1 109.7 1.0 CG C:GLU55 4.2 92.2 1.0 CB C:ASP39 4.2 102.3 1.0 N C:GLY44 4.4 109.1 1.0 OD1 C:ASN50 4.4 92.7 1.0 CA C:GLY45 4.5 113.6 1.0 CZ C:PHE49 4.5 84.1 1.0 N C:GLY45 4.5 110.9 1.0 N C:ILE42 4.6 108.9 1.0 CA C:GLY44 4.6 107.5 1.0 NE2 C:HIS61 4.7 90.9 1.0 CG2 C:THR41 4.8 104.3 1.0 CE1 C:PHE49 4.8 83.5 1.0 ND2 C:ASN50 4.9 87.6 1.0 CB C:GLU55 5.0 92.4 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