Calcium in PDB 5s5v: Tubulin-Z32386228-Complex

The structure of Tubulin-Z32386228-Complex, PDB code: 5s5v 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)	72.87 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.23, 159.54, 179.08, 90, 90, 90
R / Rfree (%)	21.7 / 26.7

The structure of Tubulin-Z32386228-Complex also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Tubulin-Z32386228-Complex (pdb code 5s5v). 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-Z32386228-Complex, PDB code: 5s5v:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z32386228-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z32386228-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:119.0 occ:1.00 OE2 A:GLU55 2.3 113.6 1.0 O A:GLY44 2.3 125.5 1.0 OG1 A:THR41 2.3 121.6 1.0 OD1 A:ASP39 2.8 120.6 1.0 OD2 A:ASP39 2.8 114.3 1.0 O A:THR41 2.9 122.5 1.0 OE1 A:GLU55 2.9 118.7 1.0 CD A:GLU55 3.0 114.6 1.0 CG A:ASP39 3.1 117.6 1.0 C A:GLY44 3.2 128.2 1.0 CB A:THR41 3.3 121.3 1.0 CA A:GLY45 3.6 136.9 1.0 C A:THR41 3.8 124.2 1.0 N A:GLY45 3.8 132.9 1.0 OD1 A:ASN50 4.0 112.3 1.0 CA A:THR41 4.0 124.6 1.0 OD2 A:ASP47 4.0 106.7 1.0 CZ A:PHE49 4.3 103.9 1.0 CA A:GLY44 4.3 125.9 1.0 N A:GLY44 4.4 121.4 1.0 N A:THR41 4.4 123.5 1.0 C A:GLY45 4.4 141.4 1.0 CG A:GLU55 4.4 110.5 1.0 CG2 A:THR41 4.6 117.0 1.0 CB A:ASP39 4.6 120.9 1.0 ND2 A:ASN50 4.6 104.2 1.0 O A:GLY45 4.6 139.4 1.0 CG A:ASN50 4.7 106.5 1.0 CE1 A:PHE49 4.8 103.2 1.0 CG A:ASP47 4.9 110.7 1.0 N A:ILE42 5.0 122.9 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z32386228-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z32386228-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:100.4 occ:1.00 O A:HOH615 2.6 89.3 1.0 OD2 E:ASP44 3.7 117.6 1.0 OG A:SER158 4.0 87.6 1.0 NZ A:LYS166 4.1 93.0 1.0 CB A:SER158 4.3 89.8 1.0 O A:GLU196 4.4 93.6 1.0 O A:GLY162 4.6 129.3 1.0 O A:HIS197 4.6 92.9 1.0 CG E:ASP44 4.7 120.9 1.0 CA A:HIS197 4.8 91.2 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z32386228-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z32386228-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:120.5 occ:1.00 OE1 B:GLU113 2.9 96.4 1.0 OE2 B:GLU113 3.7 103.3 1.0 CD B:GLU113 3.7 100.2 1.0 OE1 B:GLU110 4.5 91.0 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z32386228-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z32386228-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:92.6 occ:1.00 O C:THR41 2.3 99.6 1.0 OE2 C:GLU55 2.4 91.7 1.0 O C:GLY44 2.4 121.0 1.0 OE1 C:GLU55 2.4 99.5 1.0 OD2 C:ASP39 2.5 90.2 1.0 OD1 C:ASP39 2.5 93.6 1.0 OG1 C:THR41 2.5 100.8 1.0 O C:HOH602 2.7 88.7 1.0 CD C:GLU55 2.7 91.2 1.0 CG C:ASP39 2.8 91.3 1.0 C C:THR41 3.3 99.5 1.0 CB C:THR41 3.4 103.2 1.0 C C:GLY44 3.6 120.1 1.0 CA C:THR41 3.8 99.5 1.0 N C:THR41 4.1 95.8 1.0 CG C:GLU55 4.2 86.1 1.0 CB C:ASP39 4.3 92.2 1.0 N C:GLY44 4.4 121.0 1.0 CA C:GLY45 4.4 108.7 1.0 OD2 C:ASP47 4.4 88.9 1.0 N C:GLY45 4.4 112.5 1.0 N C:ILE42 4.5 101.1 1.0 CZ C:PHE49 4.5 80.2 1.0 CA C:GLY44 4.6 119.2 1.0 NE2 C:HIS61 4.7 83.1 1.0 OD1 C:ASN50 4.7 89.6 1.0 CG2 C:THR41 4.8 99.9 1.0 CE1 C:PHE49 4.9 78.0 1.0 CA C:ILE42 5.0 96.8 1.0 CB C:GLU55 5.0 86.7 1.0 ND2 C:ASN50 5.0 81.1 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