Calcium in PDB 5s63: Tubulin-Z2241115980-Complex

The structure of Tubulin-Z2241115980-Complex, PDB code: 5s63 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)	62.78 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.22, 159.1, 179.66, 90, 90, 90
R / Rfree (%)	21.3 / 26.8

The structure of Tubulin-Z2241115980-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z2241115980-Complex (pdb code 5s63). 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-Z2241115980-Complex, PDB code: 5s63:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2241115980-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2241115980-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:92.0 occ:1.00 O A:GLY44 2.3 99.1 1.0 O A:HOH610 2.4 94.1 1.0 O A:THR41 2.4 101.4 1.0 OE2 A:GLU55 2.5 93.2 1.0 OD1 A:ASP39 2.6 94.8 1.0 OE1 A:GLU55 2.6 95.6 1.0 OD2 A:ASP39 2.6 91.7 1.0 CD A:GLU55 2.9 93.2 1.0 CG A:ASP39 2.9 93.0 1.0 OG1 A:THR41 2.9 99.2 1.0 C A:GLY44 3.4 103.3 1.0 C A:THR41 3.5 103.2 1.0 CB A:THR41 3.5 101.8 1.0 CA A:THR41 3.9 104.0 1.0 N A:GLY44 4.1 102.6 1.0 N A:THR41 4.2 101.1 1.0 N A:GLY45 4.3 108.4 1.0 CZ A:PHE49 4.4 85.5 1.0 CA A:GLY45 4.4 112.5 1.0 CG A:GLU55 4.4 92.5 1.0 CA A:GLY44 4.4 104.3 1.0 CB A:ASP39 4.4 94.8 1.0 OD1 A:ASN50 4.5 93.5 1.0 OD2 A:ASP47 4.5 90.7 1.0 NE2 A:HIS61 4.6 93.4 1.0 N A:ILE42 4.7 101.9 1.0 ND2 A:ASN50 4.9 86.6 1.0 N A:GLY43 4.9 103.3 1.0 CE1 A:PHE49 4.9 83.9 1.0 CG2 A:THR41 5.0 90.8 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2241115980-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2241115980-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:105.7 occ:1.00 OE1 B:GLU113 2.5 96.5 1.0 OE2 B:GLU113 3.1 94.4 1.0 CD B:GLU113 3.2 96.9 1.0 OE1 B:GLU110 4.4 72.6 1.0 CG B:GLU113 4.6 85.5 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2241115980-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2241115980-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca604 b:78.4 occ:1.00 OD2 C:ASP39 2.4 71.7 1.0 O C:GLY44 2.4 92.4 1.0 OE1 C:GLU55 2.4 75.7 1.0 O C:THR41 2.4 87.2 1.0 OE2 C:GLU55 2.4 74.1 1.0 OD1 C:ASP39 2.4 74.5 1.0 OG1 C:THR41 2.6 87.2 1.0 CG C:ASP39 2.7 74.2 1.0 CD C:GLU55 2.7 73.1 1.0 C C:THR41 3.4 88.8 1.0 C C:GLY44 3.5 91.7 1.0 CB C:THR41 3.6 84.3 1.0 CA C:THR41 3.9 84.1 1.0 OD2 C:ASP47 4.0 76.5 1.0 N C:THR41 4.1 83.6 1.0 CB C:ASP39 4.2 77.6 1.0 CG C:GLU55 4.2 70.8 1.0 N C:GLY45 4.3 90.5 1.0 CA C:GLY45 4.4 89.1 1.0 N C:GLY44 4.4 91.0 1.0 OD1 C:ASN50 4.5 75.3 1.0 CA C:GLY44 4.5 90.7 1.0 NE2 C:HIS61 4.5 68.3 1.0 CZ C:PHE49 4.5 66.5 1.0 N C:ILE42 4.6 87.6 1.0 ND2 C:ASN50 4.8 66.4 1.0 CE1 C:PHE49 4.8 65.4 1.0 CG2 C:THR41 4.9 76.5 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2241115980-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2241115980-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:97.7 occ:1.00 O A:HOH628 2.8 72.0 1.0 OD2 E:ASP44 3.3 112.2 1.0 OG A:SER158 3.8 78.4 1.0 CB A:SER158 4.2 77.8 1.0 NZ A:LYS166 4.3 78.6 1.0 O A:GLU196 4.4 81.6 1.0 CG E:ASP44 4.5 115.8 1.0 O A:GLY162 4.7 102.4 1.0 CA A:SER158 5.0 76.9 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