Calcium in PDB 5s5z: Tubulin-Z2856434944-Complex

The structure of Tubulin-Z2856434944-Complex, PDB code: 5s5z 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)	91.08 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.18, 158.03, 182.1, 90, 90, 90
R / Rfree (%)	20.9 / 25.3

The structure of Tubulin-Z2856434944-Complex also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Tubulin-Z2856434944-Complex (pdb code 5s5z). 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-Z2856434944-Complex, PDB code: 5s5z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2856434944-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2856434944-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:134.5 occ:1.00 OD2 A:ASP39 2.5 107.4 1.0 CG A:ASP39 2.7 111.6 1.0 O A:THR41 2.9 133.7 1.0 CB A:ASP39 3.0 110.0 1.0 O A:ASP39 3.1 121.7 1.0 OE1 A:GLU55 3.2 110.7 1.0 CA A:ILE42 3.4 132.8 1.0 C A:THR41 3.4 135.9 1.0 OD1 A:ASP39 3.5 119.8 1.0 CD1 A:ILE42 3.5 137.3 1.0 CE1 A:HIS61 3.6 103.3 1.0 NE2 A:HIS61 3.6 102.9 1.0 N A:ILE42 3.6 133.0 1.0 C A:ASP39 3.7 120.6 1.0 CA A:ASP39 3.9 112.4 1.0 CD A:GLU55 4.0 105.4 1.0 N A:GLY43 4.1 122.9 1.0 C A:ILE42 4.2 127.4 1.0 OE2 A:GLU55 4.3 106.8 1.0 O A:GLY44 4.3 118.9 1.0 CG1 A:ILE42 4.4 131.6 1.0 N A:THR41 4.4 132.8 1.0 CB A:ILE42 4.4 133.8 1.0 CA A:THR41 4.5 133.4 1.0 OG1 A:THR41 4.5 130.1 1.0 N A:LYS40 4.8 114.6 1.0 O A:MET36 4.8 105.2 1.0 ND1 A:HIS61 4.8 103.0 1.0 N A:ASP39 4.8 111.6 1.0 N A:GLY44 4.9 120.8 1.0 CD2 A:HIS61 4.9 100.8 1.0 C A:LYS40 4.9 123.9 1.0 CG2 A:ILE42 4.9 135.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2856434944-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2856434944-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:110.4 occ:1.00 O A:HOH621 3.1 95.1 1.0 O E:HOH201 3.2 94.4 1.0 NZ A:LYS166 3.3 77.8 1.0 OD1 A:ASP199 3.7 90.3 1.0 OG A:SER158 4.0 85.2 1.0 O A:HIS197 4.0 84.0 1.0 OD2 A:ASP199 4.1 82.6 1.0 O A:LYS164 4.3 95.8 1.0 CG A:ASP199 4.3 84.2 1.0 O A:GLY162 4.4 110.8 1.0 CE A:LYS166 4.5 78.4 1.0 C A:HIS197 4.6 82.3 1.0 CA A:HIS197 4.7 83.1 1.0 CB A:SER158 4.7 82.6 1.0 O A:GLU196 4.9 88.6 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2856434944-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2856434944-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:114.2 occ:1.00 OE1 B:GLU113 2.7 85.7 1.0 OE2 B:GLU113 3.0 93.3 1.0 CD B:GLU113 3.2 91.0 1.0 OE1 B:GLU110 4.6 81.9 1.0 CG B:GLU113 4.7 79.4 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2856434944-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2856434944-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:80.9 occ:1.00 OG1 C:THR41 2.3 88.9 1.0 O C:GLY44 2.4 83.9 1.0 O C:HOH633 2.4 75.6 1.0 OE2 C:GLU55 2.4 78.0 1.0 O C:THR41 2.4 85.8 1.0 OD1 C:ASP39 2.5 78.9 1.0 OD2 C:ASP39 2.5 75.2 1.0 OE1 C:GLU55 2.8 74.2 1.0 CG C:ASP39 2.8 78.6 1.0 CD C:GLU55 3.0 73.6 1.0 C C:THR41 3.4 84.3 1.0 CB C:THR41 3.5 84.1 1.0 C C:GLY44 3.5 85.7 1.0 CA C:THR41 3.9 84.8 1.0 N C:THR41 4.1 84.9 1.0 CA C:GLY45 4.1 91.8 1.0 N C:GLY45 4.2 91.0 1.0 CB C:ASP39 4.3 78.0 1.0 CG C:GLU55 4.5 72.4 1.0 N C:GLY44 4.5 85.5 1.0 CA C:GLY44 4.6 83.8 1.0 N C:ILE42 4.6 89.5 1.0 OD2 C:ASP47 4.6 88.6 1.0 CZ C:PHE49 4.6 69.7 1.0 CG2 C:THR41 4.7 77.7 1.0 NE2 C:HIS61 4.8 69.0 1.0 OD1 C:ASN50 4.8 80.8 1.0 ND2 C:ASN50 4.9 66.2 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