Calcium in PDB 5s59: Tubulin-Z1324080698-Complex

The structure of Tubulin-Z1324080698-Complex, PDB code: 5s59 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)	59.84 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.56, 158.9, 179.33, 90, 90, 90
R / Rfree (%)	22 / 26.8

The structure of Tubulin-Z1324080698-Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Tubulin-Z1324080698-Complex (pdb code 5s59). 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-Z1324080698-Complex, PDB code: 5s59:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:126.9 occ:1.00 O A:HOH617 2.3 110.5 1.0 OD2 A:ASP39 2.3 109.1 1.0 OG1 A:THR41 2.3 111.5 1.0 O A:THR41 2.4 113.8 1.0 OE2 A:GLU55 2.4 104.8 1.0 OD1 A:ASP39 2.4 108.8 1.0 O A:GLY44 2.4 124.8 1.0 OE1 A:GLU55 2.7 109.6 1.0 CG A:ASP39 2.7 110.3 1.0 CD A:GLU55 2.9 105.2 1.0 C A:THR41 3.4 113.8 1.0 CB A:THR41 3.4 113.0 1.0 C A:GLY44 3.6 123.9 1.0 CA A:THR41 3.8 114.0 1.0 CZ A:PHE49 4.1 97.7 1.0 N A:THR41 4.1 113.8 1.0 CB A:ASP39 4.2 109.8 1.0 N A:GLY44 4.3 119.2 1.0 CG A:GLU55 4.4 101.7 1.0 CA A:GLY45 4.4 124.0 1.0 N A:GLY45 4.4 123.3 1.0 OD2 A:ASP47 4.4 108.0 1.0 CA A:GLY44 4.5 122.6 1.0 N A:ILE42 4.5 112.0 1.0 OD1 A:ASN50 4.7 109.4 1.0 CG2 A:THR41 4.7 110.1 1.0 CE1 A:PHE49 4.7 94.3 1.0 NE2 A:HIS61 4.9 103.4 1.0 ND2 A:ASN50 4.9 102.9 1.0 N A:GLY43 5.0 111.9 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:131.2 occ:1.00 OE1 B:GLU113 2.4 100.8 1.0 CD B:GLU113 3.2 99.8 1.0 OE2 B:GLU113 3.2 96.4 1.0 OE1 B:GLU110 4.6 85.2 1.0 CG B:GLU113 4.6 91.8 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:96.1 occ:1.00 O C:GLY44 2.4 102.6 1.0 OE2 C:GLU55 2.4 90.3 1.0 OD2 C:ASP39 2.4 95.0 1.0 OE1 C:GLU55 2.4 99.1 1.0 O C:THR41 2.4 103.4 1.0 OG1 C:THR41 2.5 101.7 1.0 OD1 C:ASP39 2.5 99.8 1.0 CD C:GLU55 2.7 93.9 1.0 CG C:ASP39 2.8 96.1 1.0 C C:THR41 3.4 104.9 1.0 CB C:THR41 3.5 102.5 1.0 C C:GLY44 3.5 101.9 1.0 OD2 C:ASP47 3.9 95.9 1.0 CA C:THR41 3.9 105.1 1.0 N C:THR41 4.2 103.6 1.0 CG C:GLU55 4.2 88.9 1.0 CA C:GLY45 4.3 102.2 1.0 CB C:ASP39 4.3 98.5 1.0 N C:GLY45 4.3 102.0 1.0 N C:GLY44 4.4 106.1 1.0 CZ C:PHE49 4.5 84.8 1.0 OD1 C:ASN50 4.5 87.8 1.0 CA C:GLY44 4.5 103.6 1.0 N C:ILE42 4.6 104.6 1.0 CG2 C:THR41 4.8 101.3 1.0 NE2 C:HIS61 4.9 89.6 1.0 ND2 C:ASN50 4.9 83.9 1.0 CE1 C:PHE49 4.9 82.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:108.1 occ:1.00 OD2 E:ASP44 3.4 124.3 1.0 OG A:SER158 4.0 86.9 1.0 O A:GLU196 4.0 91.3 1.0 NZ A:LYS166 4.3 81.8 1.0 CB A:SER158 4.4 88.2 1.0 CG E:ASP44 4.5 125.9 1.0 CA A:HIS197 4.6 87.0 1.0 O A:GLY162 4.8 114.4 1.0 O A:HIS197 4.8 86.5 1.0 OD1 A:ASP199 4.8 93.9 1.0 OD1 E:ASP44 4.8 123.0 1.0 C A:HIS197 4.9 88.0 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