Calcium in PDB 5s4m: Tubulin-Z2142244288-Complex

The structure of Tubulin-Z2142244288-Complex, PDB code: 5s4m 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)	63.02 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.67, 157.87, 179.17, 90, 90, 90
R / Rfree (%)	20.6 / 24.4

The structure of Tubulin-Z2142244288-Complex also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Tubulin-Z2142244288-Complex (pdb code 5s4m). 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-Z2142244288-Complex, PDB code: 5s4m:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:89.1 occ:1.00 O A:GLY44 2.3 95.5 1.0 OD2 A:ASP39 2.4 85.0 1.0 OD1 A:ASP39 2.4 90.4 1.0 O A:HOH611 2.5 88.2 1.0 OE2 A:GLU55 2.5 86.7 1.0 OG1 A:THR41 2.5 88.4 1.0 O A:THR41 2.5 99.0 1.0 CG A:ASP39 2.7 88.8 1.0 OE1 A:GLU55 2.8 93.8 1.0 CD A:GLU55 3.0 87.3 1.0 CB A:THR41 3.5 93.0 1.0 C A:GLY44 3.5 99.7 1.0 C A:THR41 3.6 98.5 1.0 CA A:THR41 3.9 98.8 1.0 CA A:GLY45 4.1 101.7 1.0 CB A:ASP39 4.2 89.3 1.0 N A:THR41 4.2 100.8 1.0 N A:GLY45 4.2 102.5 1.0 CZ A:PHE49 4.3 77.6 1.0 OD1 A:ASN50 4.4 85.7 1.0 OD2 A:ASP47 4.4 85.7 1.0 CG A:GLU55 4.5 85.4 1.0 N A:GLY44 4.5 99.4 1.0 CA A:GLY44 4.6 99.9 1.0 ND2 A:ASN50 4.7 78.8 1.0 N A:ILE42 4.7 103.5 1.0 NE2 A:HIS61 4.8 82.7 1.0 CG2 A:THR41 4.8 83.5 1.0 CE1 A:PHE49 4.9 76.9 1.0 C A:GLY45 5.0 99.0 1.0 CA A:ASP39 5.0 91.3 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:90.5 occ:1.00 O A:HOH664 2.8 71.2 1.0 O A:HOH641 3.6 65.2 1.0 OD2 E:ASP44 3.6 96.2 1.0 OG A:SER158 3.7 63.2 1.0 O A:GLU196 4.0 69.1 1.0 O A:HOH668 4.1 79.8 1.0 NZ A:LYS166 4.2 56.3 1.0 CB A:SER158 4.2 61.8 1.0 CA A:HIS197 4.6 62.3 1.0 O A:HIS197 4.6 64.7 1.0 CG E:ASP44 4.8 97.2 1.0 O A:GLY162 4.8 88.5 1.0 C A:HIS197 4.9 63.8 1.0 ND1 A:HIS197 5.0 67.9 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:110.0 occ:1.00 OE1 B:GLU113 2.7 85.6 1.0 CD B:GLU113 3.4 85.4 1.0 OE2 B:GLU113 3.5 86.5 1.0 OE1 B:GLU110 4.4 56.4 1.0 CG B:GLU113 4.8 70.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:70.8 occ:1.00 O C:GLY44 2.3 74.7 1.0 OE2 C:GLU55 2.4 65.8 1.0 OG1 C:THR41 2.4 71.6 1.0 O C:HOH602 2.5 62.1 1.0 O C:THR41 2.5 76.0 1.0 OE1 C:GLU55 2.5 64.0 1.0 OD2 C:ASP39 2.5 69.7 1.0 OD1 C:ASP39 2.6 71.5 1.0 CD C:GLU55 2.8 65.4 1.0 CG C:ASP39 2.9 69.5 1.0 CB C:THR41 3.4 73.4 1.0 C C:THR41 3.5 77.4 1.0 C C:GLY44 3.5 76.5 1.0 CA C:THR41 3.9 71.5 1.0 CA C:GLY45 4.0 75.9 1.0 OD2 C:ASP47 4.1 75.8 1.0 N C:THR41 4.2 73.5 1.0 N C:GLY45 4.2 76.5 1.0 CG C:GLU55 4.3 61.5 1.0 CB C:ASP39 4.4 71.7 1.0 CZ C:PHE49 4.5 60.1 1.0 OD1 C:ASN50 4.6 60.4 1.0 N C:ILE42 4.6 76.4 1.0 N C:GLY44 4.6 80.4 1.0 CA C:GLY44 4.6 79.5 1.0 NE2 C:HIS61 4.7 59.3 1.0 CG2 C:THR41 4.8 61.5 1.0 ND2 C:ASN50 4.8 58.3 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