Calcium in PDB 5s53: Tubulin-Z1349163663-Complex

The structure of Tubulin-Z1349163663-Complex, PDB code: 5s53 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)	68.19 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.32, 159.31, 178.96, 90, 90, 90
R / Rfree (%)	21.8 / 26.7

The structure of Tubulin-Z1349163663-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1349163663-Complex (pdb code 5s53). 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-Z1349163663-Complex, PDB code: 5s53:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1349163663-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1349163663-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:114.7 occ:1.00 OE2 A:GLU55 2.3 107.9 1.0 O A:GLY44 2.3 126.4 1.0 OG1 A:THR41 2.3 118.1 1.0 OD2 A:ASP39 2.5 108.8 1.0 OD1 A:ASP39 2.7 111.0 1.0 OE1 A:GLU55 2.7 118.0 1.0 CD A:GLU55 2.9 111.5 1.0 O A:THR41 2.9 118.3 1.0 CG A:ASP39 2.9 110.0 1.0 C A:GLY44 3.3 128.5 1.0 CB A:THR41 3.5 117.7 1.0 C A:THR41 3.8 120.6 1.0 CA A:GLY45 3.9 136.2 1.0 CZ A:PHE49 4.0 94.8 1.0 N A:GLY45 4.0 134.9 1.0 OD1 A:ASN50 4.1 105.0 1.0 CA A:THR41 4.1 117.9 1.0 OD2 A:ASP47 4.2 97.7 1.0 N A:GLY44 4.3 127.7 1.0 CG A:GLU55 4.3 106.5 1.0 N A:THR41 4.4 115.1 1.0 CA A:GLY44 4.4 127.9 1.0 CE1 A:PHE49 4.4 94.5 1.0 CB A:ASP39 4.4 109.5 1.0 C A:GLY45 4.6 137.3 1.0 ND2 A:ASN50 4.7 96.5 1.0 CG2 A:THR41 4.7 112.3 1.0 O A:GLY45 4.7 133.8 1.0 CG A:ASN50 4.8 101.9 1.0 NE2 A:HIS61 4.9 105.5 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1349163663-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1349163663-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:107.2 occ:1.00 O E:HOH201 2.8 102.7 1.0 OD2 E:ASP44 3.6 141.8 1.0 OG A:SER158 3.8 86.6 1.0 NZ A:LYS166 3.9 87.7 1.0 O A:GLY162 4.0 131.8 1.0 CB A:SER158 4.2 86.5 1.0 O A:GLU196 4.6 100.2 1.0 CG E:ASP44 4.7 144.1 1.0 CA A:SER158 4.8 85.7 1.0 CE A:LYS166 4.9 76.1 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1349163663-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1349163663-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:115.8 occ:1.00 OE1 B:GLU113 2.8 101.7 1.0 CD B:GLU113 3.6 101.2 1.0 OE2 B:GLU113 3.7 103.5 1.0 OE1 B:GLU110 4.3 84.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1349163663-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1349163663-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:91.6 occ:1.00 OG1 C:THR41 2.3 93.8 1.0 OD2 C:ASP39 2.3 88.4 1.0 OE1 C:GLU55 2.4 92.7 1.0 O C:THR41 2.4 97.2 1.0 OD1 C:ASP39 2.4 92.0 1.0 OE2 C:GLU55 2.5 86.0 1.0 O C:GLY44 2.5 98.7 1.0 CG C:ASP39 2.7 92.7 1.0 CD C:GLU55 2.7 87.5 1.0 O C:HOH601 2.8 85.1 1.0 CB C:THR41 3.4 97.3 1.0 C C:THR41 3.4 97.7 1.0 C C:GLY44 3.7 100.9 1.0 CA C:THR41 3.7 100.5 1.0 N C:THR41 4.0 96.8 1.0 CB C:ASP39 4.2 95.5 1.0 CG C:GLU55 4.3 85.5 1.0 OD2 C:ASP47 4.5 82.1 1.0 CA C:GLY45 4.5 101.1 1.0 N C:GLY44 4.5 103.2 1.0 N C:GLY45 4.5 105.2 1.0 N C:ILE42 4.6 95.0 1.0 CZ C:PHE49 4.6 77.0 1.0 CG2 C:THR41 4.7 94.9 1.0 CA C:GLY44 4.7 101.7 1.0 NE2 C:HIS61 4.7 85.3 1.0 OD1 C:ASN50 4.8 85.7 1.0 ND2 C:ASN50 4.8 80.3 1.0 CE1 C:PHE49 4.9 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