Calcium in PDB 5s54: Tubulin-Z2856434816-Complex

The structure of Tubulin-Z2856434816-Complex, PDB code: 5s54 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)	71.96 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.33, 157.15, 179.17, 90, 90, 90
R / Rfree (%)	20.6 / 25

The structure of Tubulin-Z2856434816-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z2856434816-Complex (pdb code 5s54). 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-Z2856434816-Complex, PDB code: 5s54:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2856434816-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2856434816-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:115.9 occ:1.00 OD1 A:ASP39 2.3 110.4 1.0 OE2 A:GLU55 2.4 107.3 1.0 OD2 A:ASP39 2.4 106.0 1.0 OG1 A:THR41 2.4 113.8 1.0 O A:GLY44 2.4 116.5 1.0 O A:THR41 2.4 120.7 1.0 O A:HOH604 2.5 105.3 1.0 OE1 A:GLU55 2.6 111.5 1.0 CG A:ASP39 2.7 109.2 1.0 CD A:GLU55 2.8 108.4 1.0 C A:THR41 3.5 119.7 1.0 CB A:THR41 3.5 114.3 1.0 C A:GLY44 3.6 117.4 1.0 CA A:THR41 3.9 117.4 1.0 N A:THR41 4.1 118.9 1.0 CB A:ASP39 4.2 106.4 1.0 CA A:GLY45 4.2 112.5 1.0 CZ A:PHE49 4.3 94.0 1.0 CG A:GLU55 4.3 104.0 1.0 N A:GLY45 4.3 117.4 1.0 OD1 A:ASN50 4.4 102.9 1.0 N A:GLY44 4.6 117.2 1.0 OD2 A:ASP47 4.6 106.3 1.0 CA A:GLY44 4.6 117.4 1.0 N A:ILE42 4.7 121.5 1.0 CG2 A:THR41 4.8 107.5 1.0 ND2 A:ASN50 4.8 95.0 1.0 NE2 A:HIS61 4.9 100.4 1.0 CE1 A:PHE49 4.9 90.5 1.0 CA A:ASP39 5.0 110.2 1.0 C A:GLY45 5.0 111.5 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2856434816-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2856434816-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:106.1 occ:1.00 O E:HOH205 2.3 96.4 1.0 O A:HOH632 2.7 80.8 1.0 O A:HOH627 3.2 72.1 1.0 O A:HOH625 3.6 91.6 1.0 OG A:SER158 3.7 80.7 1.0 OD2 E:ASP44 3.9 114.7 1.0 NZ A:LYS166 3.9 72.8 1.0 CB A:SER158 4.3 76.3 1.0 O A:GLU196 4.4 83.5 1.0 O A:GLY162 4.4 102.2 1.0 CA A:HIS197 4.7 76.8 1.0 O A:HIS197 4.7 76.1 1.0 OD1 A:ASP199 4.9 77.9 1.0 CE A:LYS166 4.9 64.9 1.0 CA A:SER158 4.9 75.8 1.0 CG E:ASP44 4.9 112.4 1.0 C A:HIS197 4.9 75.1 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2856434816-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2856434816-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:120.0 occ:1.00 OE1 B:GLU113 2.5 105.9 1.0 CD B:GLU113 3.2 104.9 1.0 OE2 B:GLU113 3.2 98.0 1.0 CG B:GLU113 4.7 90.2 1.0 OE1 B:GLU110 4.7 72.1 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2856434816-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2856434816-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:94.6 occ:1.00 O C:GLY44 2.3 102.8 1.0 OE2 C:GLU55 2.4 88.5 1.0 O C:HOH617 2.4 82.8 1.0 OG1 C:THR41 2.5 101.0 1.0 O C:THR41 2.5 102.7 1.0 OE1 C:GLU55 2.5 93.1 1.0 OD2 C:ASP39 2.5 84.7 1.0 CD C:GLU55 2.8 85.7 1.0 OD1 C:ASP39 2.9 90.6 1.0 CG C:ASP39 3.0 89.7 1.0 CB C:THR41 3.4 96.4 1.0 C C:THR41 3.4 99.5 1.0 C C:GLY44 3.5 103.5 1.0 CA C:THR41 3.8 97.0 1.0 N C:THR41 4.2 101.1 1.0 CA C:GLY45 4.3 103.9 1.0 CG C:GLU55 4.3 78.1 1.0 OD2 C:ASP47 4.3 89.5 1.0 N C:GLY45 4.3 102.6 1.0 N C:ILE42 4.5 100.6 1.0 N C:GLY44 4.5 107.9 1.0 CB C:ASP39 4.5 91.2 1.0 CZ C:PHE49 4.6 78.5 1.0 CA C:GLY44 4.6 108.7 1.0 OD1 C:ASN50 4.6 79.2 1.0 CG2 C:THR41 4.7 82.0 1.0 NE2 C:HIS61 4.9 79.7 1.0 ND2 C:ASN50 5.0 74.0 1.0 CA C:ILE42 5.0 93.1 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