Calcium in PDB 5s4x: Tubulin-Z2856434917-Complex

The structure of Tubulin-Z2856434917-Complex, PDB code: 5s4x 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)	72.84 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.11, 159.22, 180.52, 90, 90, 90
R / Rfree (%)	20.2 / 24.5

The structure of Tubulin-Z2856434917-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z2856434917-Complex (pdb code 5s4x). 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-Z2856434917-Complex, PDB code: 5s4x:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2856434917-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2856434917-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:127.6 occ:1.00 O A:GLY44 2.3 133.1 1.0 OE2 A:GLU55 2.4 124.2 1.0 OG1 A:THR41 2.5 133.0 1.0 OD2 A:ASP39 2.7 121.1 1.0 OD1 A:ASP39 2.7 130.9 1.0 CG A:ASP39 3.0 124.1 1.0 O A:THR41 3.0 137.2 1.0 CD A:GLU55 3.1 126.1 1.0 OE1 A:GLU55 3.1 131.2 1.0 C A:GLY44 3.4 135.0 1.0 OD2 A:ASP47 3.5 122.1 1.0 CA A:GLY45 3.7 133.3 1.0 CB A:THR41 3.7 135.8 1.0 OD1 A:ASN50 3.8 119.2 1.0 N A:GLY45 3.9 133.3 1.0 C A:THR41 4.0 135.7 1.0 CZ A:PHE49 4.1 107.6 1.0 CA A:THR41 4.3 135.4 1.0 ND2 A:ASN50 4.4 108.3 1.0 C A:GLY45 4.4 133.2 1.0 CB A:ASP39 4.5 129.2 1.0 N A:THR41 4.5 132.6 1.0 CG A:ASP47 4.5 123.3 1.0 CG A:ASN50 4.5 109.6 1.0 CG A:GLU55 4.5 120.3 1.0 CE1 A:PHE49 4.6 101.3 1.0 CA A:GLY44 4.6 137.2 1.0 N A:GLY44 4.6 136.6 1.0 O A:GLY45 4.7 130.0 1.0 CG2 A:THR41 4.9 126.5 1.0 NE2 A:HIS61 5.0 107.0 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2856434917-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2856434917-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:109.8 occ:1.00 O A:HOH622 2.3 91.9 1.0 O E:HOH201 2.8 107.2 1.0 O A:HOH607 3.2 78.3 1.0 OD1 A:ASP199 3.6 92.2 1.0 O A:HIS197 3.6 92.4 1.0 O A:GLU196 4.1 110.0 1.0 C A:HIS197 4.1 97.2 1.0 NZ A:LYS166 4.2 86.8 1.0 CA A:HIS197 4.2 99.5 1.0 OG A:SER158 4.4 88.5 1.0 CG A:ASP199 4.5 89.8 1.0 OD2 E:ASP44 4.6 135.9 1.0 OD2 A:ASP199 4.6 90.0 1.0 C A:GLU196 4.8 105.1 1.0 N A:HIS197 4.9 102.1 1.0 CE A:LYS166 5.0 85.7 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2856434917-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2856434917-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:114.9 occ:1.00 OE1 B:GLU113 2.3 108.3 1.0 OE2 B:GLU113 2.9 109.0 1.0 CD B:GLU113 2.9 109.0 1.0 CG B:GLU113 4.4 92.0 1.0 OE1 B:GLU110 4.5 90.2 1.0 CB B:GLU113 5.0 88.4 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2856434917-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2856434917-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:103.5 occ:1.00 O C:GLY44 2.4 114.1 1.0 OD1 C:ASP39 2.4 109.2 1.0 OE2 C:GLU55 2.5 98.2 1.0 OD2 C:ASP39 2.5 103.5 1.0 OG1 C:THR41 2.5 104.9 1.0 O C:THR41 2.6 109.5 1.0 OE1 C:GLU55 2.6 99.6 1.0 CG C:ASP39 2.8 106.2 1.0 CD C:GLU55 2.9 96.5 1.0 CB C:THR41 3.4 105.9 1.0 C C:THR41 3.5 109.5 1.0 C C:GLY44 3.5 113.5 1.0 CA C:THR41 3.9 106.3 1.0 OD2 C:ASP47 4.1 100.7 1.0 N C:THR41 4.2 106.7 1.0 CB C:ASP39 4.3 105.8 1.0 CA C:GLY45 4.3 100.6 1.0 N C:GLY45 4.3 104.3 1.0 CG C:GLU55 4.4 87.6 1.0 CZ C:PHE49 4.5 84.2 1.0 N C:GLY44 4.5 115.5 1.0 OD1 C:ASN50 4.5 86.5 1.0 CA C:GLY44 4.6 115.1 1.0 N C:ILE42 4.7 112.3 1.0 CG2 C:THR41 4.7 95.1 1.0 NE2 C:HIS61 4.7 86.1 1.0 CE1 C:PHE49 4.9 86.1 1.0 ND2 C:ASN50 4.9 83.9 1.0 CA C:ASP39 5.0 109.4 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