Calcium in PDB 5s5j: Tubulin-Z1148747945-Complex

The structure of Tubulin-Z1148747945-Complex, PDB code: 5s5j 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)	62.71 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.77, 159.73, 179.63, 90, 90, 90
R / Rfree (%)	20.5 / 23.8

The structure of Tubulin-Z1148747945-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1148747945-Complex (pdb code 5s5j). 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-Z1148747945-Complex, PDB code: 5s5j:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1148747945-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1148747945-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:92.7 occ:1.00 O A:GLY44 2.3 94.2 1.0 OD2 A:ASP39 2.4 88.3 1.0 OE2 A:GLU55 2.4 87.9 1.0 OD1 A:ASP39 2.5 93.8 1.0 OG1 A:THR41 2.5 92.7 1.0 CG A:ASP39 2.7 90.7 1.0 OE1 A:GLU55 2.7 93.6 1.0 O A:THR41 2.8 97.6 1.0 CD A:GLU55 2.9 92.0 1.0 C A:GLY44 3.4 96.4 1.0 CB A:THR41 3.5 98.0 1.0 C A:THR41 3.7 99.5 1.0 CA A:THR41 4.0 100.4 1.0 CA A:GLY45 4.0 99.5 1.0 OD2 A:ASP47 4.1 88.0 1.0 N A:GLY45 4.1 97.0 1.0 CZ A:PHE49 4.2 80.0 1.0 OD1 A:ASN50 4.2 88.4 1.0 CB A:ASP39 4.2 92.2 1.0 N A:THR41 4.3 99.6 1.0 N A:GLY44 4.4 98.2 1.0 CG A:GLU55 4.4 85.7 1.0 CA A:GLY44 4.5 97.5 1.0 ND2 A:ASN50 4.5 81.8 1.0 CG2 A:THR41 4.8 88.5 1.0 CE1 A:PHE49 4.8 76.3 1.0 C A:GLY45 4.8 98.5 1.0 CG A:ASN50 4.8 82.0 1.0 NE2 A:HIS61 4.8 84.3 1.0 O A:GLY45 5.0 97.7 1.0 N A:ILE42 5.0 98.7 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1148747945-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1148747945-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:92.8 occ:1.00 O E:HOH201 2.4 81.7 1.0 O A:HOH655 3.0 68.9 1.0 O A:HOH617 3.3 58.8 1.0 OD2 E:ASP44 3.8 105.1 1.0 OG A:SER158 3.8 65.9 1.0 NZ A:LYS166 4.1 61.1 1.0 CB A:SER158 4.2 66.0 1.0 O A:GLY162 4.3 91.0 1.0 O A:GLU196 4.6 69.2 1.0 O A:HIS197 4.8 63.5 1.0 CA A:SER158 4.8 66.1 1.0 CG E:ASP44 4.9 102.9 1.0 CA A:HIS197 4.9 65.1 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1148747945-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1148747945-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:113.0 occ:1.00 OE1 B:GLU113 2.6 72.5 1.0 CD B:GLU113 3.4 77.8 1.0 OE2 B:GLU113 3.5 79.7 1.0 OE1 B:GLU110 4.6 55.2 1.0 CG B:GLU113 4.8 71.0 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1148747945-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1148747945-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:65.1 occ:1.00 OE1 C:GLU55 2.3 60.3 1.0 O C:GLY44 2.4 65.0 1.0 O C:THR41 2.4 67.2 1.0 OD2 C:ASP39 2.4 60.2 1.0 OG1 C:THR41 2.5 68.8 1.0 OE2 C:GLU55 2.5 58.4 1.0 OD1 C:ASP39 2.5 64.0 1.0 O C:HOH602 2.7 59.3 1.0 CD C:GLU55 2.7 58.9 1.0 CG C:ASP39 2.8 63.2 1.0 C C:THR41 3.4 71.4 1.0 C C:GLY44 3.5 67.1 1.0 CB C:THR41 3.5 72.2 1.0 CA C:THR41 3.9 71.4 1.0 N C:THR41 4.2 67.8 1.0 CG C:GLU55 4.2 54.8 1.0 CB C:ASP39 4.3 66.0 1.0 N C:GLY44 4.3 70.0 1.0 N C:GLY45 4.3 73.6 1.0 CA C:GLY45 4.3 71.7 1.0 CA C:GLY44 4.5 68.3 1.0 OD2 C:ASP47 4.5 68.8 1.0 NE2 C:HIS61 4.5 55.8 1.0 N C:ILE42 4.6 69.1 1.0 OD1 C:ASN50 4.7 58.4 1.0 CZ C:PHE49 4.7 53.8 1.0 CG2 C:THR41 4.8 61.8 1.0 O C:HOH669 4.9 61.7 1.0 ND2 C:ASN50 5.0 52.9 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