Calcium in PDB 5s4r: Tubulin-Z117233350-Complex

The structure of Tubulin-Z117233350-Complex, PDB code: 5s4r 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)	62.92 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.36, 159.89, 180.03, 90, 90, 90
R / Rfree (%)	21.4 / 25.1

The structure of Tubulin-Z117233350-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z117233350-Complex (pdb code 5s4r). 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-Z117233350-Complex, PDB code: 5s4r:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z117233350-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z117233350-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:98.6 occ:1.00 O A:HOH602 2.3 97.5 1.0 OG1 A:THR41 2.3 100.5 1.0 O A:GLY44 2.3 104.3 1.0 OD2 A:ASP39 2.3 94.1 1.0 OE2 A:GLU55 2.4 99.7 1.0 OD1 A:ASP39 2.5 102.5 1.0 O A:THR41 2.6 103.2 1.0 OE1 A:GLU55 2.8 102.1 1.0 CG A:ASP39 2.8 98.9 1.0 CD A:GLU55 2.9 99.5 1.0 C A:GLY44 3.4 103.4 1.0 CB A:THR41 3.5 100.2 1.0 C A:THR41 3.6 105.7 1.0 CA A:THR41 4.0 105.1 1.0 CA A:GLY45 4.1 111.6 1.0 N A:GLY45 4.1 108.6 1.0 N A:THR41 4.2 102.5 1.0 CZ A:PHE49 4.2 86.6 1.0 CB A:ASP39 4.3 101.2 1.0 OD2 A:ASP47 4.3 92.2 1.0 N A:GLY44 4.3 103.0 1.0 OD1 A:ASN50 4.4 96.4 1.0 CG A:GLU55 4.4 95.0 1.0 CA A:GLY44 4.4 101.9 1.0 CG2 A:THR41 4.7 98.9 1.0 NE2 A:HIS61 4.7 93.5 1.0 N A:ILE42 4.8 100.9 1.0 ND2 A:ASN50 4.8 90.5 1.0 CE1 A:PHE49 4.9 87.7 1.0 C A:GLY45 4.9 115.6 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z117233350-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z117233350-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:115.8 occ:1.00 OE1 B:GLU113 2.7 87.9 1.0 CD B:GLU113 3.5 86.4 1.0 OE2 B:GLU113 3.6 85.6 1.0 OE1 B:GLU110 4.1 70.9 1.0 OE2 B:GLU110 4.8 75.6 1.0 CD B:GLU110 4.9 71.5 1.0 CG B:GLU113 5.0 79.7 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z117233350-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z117233350-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:77.4 occ:1.00 O C:GLY44 2.3 84.2 1.0 OE1 C:GLU55 2.3 76.2 1.0 O C:THR41 2.3 82.0 1.0 OG1 C:THR41 2.4 81.9 1.0 OD2 C:ASP39 2.4 71.0 1.0 OD1 C:ASP39 2.5 77.3 1.0 OE2 C:GLU55 2.5 70.7 1.0 O C:HOH601 2.7 71.3 1.0 CD C:GLU55 2.8 73.0 1.0 CG C:ASP39 2.8 75.0 1.0 C C:THR41 3.4 84.4 1.0 CB C:THR41 3.4 83.5 1.0 C C:GLY44 3.5 83.9 1.0 CA C:THR41 3.8 85.1 1.0 N C:THR41 4.1 80.7 1.0 N C:GLY44 4.2 85.9 1.0 CG C:GLU55 4.3 69.2 1.0 N C:GLY45 4.3 81.9 1.0 CA C:GLY45 4.3 83.3 1.0 CB C:ASP39 4.3 78.0 1.0 OD2 C:ASP47 4.4 75.8 1.0 CA C:GLY44 4.4 85.1 1.0 N C:ILE42 4.6 82.3 1.0 OD1 C:ASN50 4.7 75.6 1.0 CZ C:PHE49 4.7 66.2 1.0 CG2 C:THR41 4.7 79.6 1.0 NE2 C:HIS61 4.7 69.6 1.0 ND2 C:ASN50 5.0 65.7 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z117233350-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z117233350-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:107.9 occ:1.00 OD2 E:ASP44 3.2 113.9 1.0 O A:HOH622 3.5 71.9 1.0 OG A:SER158 3.9 77.2 1.0 CB A:SER158 4.2 79.0 1.0 O A:HOH646 4.3 85.7 1.0 O A:GLU196 4.4 83.7 1.0 NZ A:LYS166 4.4 69.9 1.0 CG E:ASP44 4.4 117.4 1.0 O A:GLY162 4.5 107.8 1.0 CA A:HIS197 4.9 78.0 1.0 CA A:SER158 5.0 77.4 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