Calcium in PDB 5s5i: Tubulin-Z295848548-Complex

The structure of Tubulin-Z295848548-Complex, PDB code: 5s5i 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)	62.66 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.89, 158.87, 179.47, 90, 90, 90
R / Rfree (%)	21.2 / 25.9

The structure of Tubulin-Z295848548-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z295848548-Complex (pdb code 5s5i). 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-Z295848548-Complex, PDB code: 5s5i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z295848548-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z295848548-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:103.6 occ:1.00 OE2 A:GLU55 2.3 94.0 1.0 O A:GLY44 2.3 102.7 1.0 OD2 A:ASP39 2.3 97.3 1.0 OD1 A:ASP39 2.4 100.3 1.0 OG1 A:THR41 2.5 103.8 1.0 CG A:ASP39 2.7 101.8 1.0 O A:THR41 2.7 104.1 1.0 CD A:GLU55 3.0 98.0 1.0 OE1 A:GLU55 3.1 98.7 1.0 C A:GLY44 3.4 105.7 1.0 CB A:THR41 3.5 103.5 1.0 C A:THR41 3.7 105.9 1.0 OD2 A:ASP47 3.9 98.4 1.0 CA A:GLY45 4.0 113.6 1.0 CA A:THR41 4.0 106.0 1.0 CZ A:PHE49 4.0 90.2 1.0 N A:GLY45 4.1 107.8 1.0 CB A:ASP39 4.2 103.0 1.0 OD1 A:ASN50 4.2 100.3 1.0 N A:THR41 4.3 105.7 1.0 N A:GLY44 4.4 108.9 1.0 CG A:GLU55 4.5 96.6 1.0 CE1 A:PHE49 4.5 88.5 1.0 CA A:GLY44 4.5 104.8 1.0 ND2 A:ASN50 4.6 94.6 1.0 NE2 A:HIS61 4.8 96.8 1.0 CG2 A:THR41 4.8 92.5 1.0 C A:GLY45 4.8 118.2 1.0 CG A:ASN50 4.9 96.6 1.0 N A:ILE42 4.9 107.6 1.0 CG A:ASP47 5.0 102.4 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z295848548-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z295848548-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:99.9 occ:1.00 O E:HOH202 2.9 90.5 1.0 O A:HOH619 3.2 72.8 1.0 O A:HOH637 3.2 79.5 1.0 NZ A:LYS166 3.8 77.6 1.0 OD2 E:ASP44 3.8 115.8 1.0 OG A:SER158 3.9 81.3 1.0 O A:GLY162 4.0 101.4 1.0 CB A:SER158 4.3 78.5 1.0 O A:GLU196 4.7 81.3 1.0 CA A:SER158 4.8 79.0 1.0 CG E:ASP44 4.9 113.6 1.0 O A:LYS164 4.9 90.2 1.0 CE A:LYS166 5.0 72.1 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z295848548-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z295848548-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:116.5 occ:1.00 OE1 B:GLU113 2.8 85.5 1.0 OE2 B:GLU113 3.4 95.9 1.0 CD B:GLU113 3.5 90.2 1.0 OE1 B:GLU110 4.8 62.5 1.0 CG B:GLU113 4.9 80.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z295848548-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z295848548-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:83.4 occ:1.00 O C:GLY44 2.3 95.6 1.0 OE1 C:GLU55 2.3 82.5 1.0 OE2 C:GLU55 2.3 72.2 1.0 O C:THR41 2.4 84.7 1.0 O C:HOH607 2.4 76.2 1.0 OD2 C:ASP39 2.5 74.4 1.0 OG1 C:THR41 2.6 88.5 1.0 OD1 C:ASP39 2.7 82.9 1.0 CD C:GLU55 2.7 76.9 1.0 CG C:ASP39 2.9 78.9 1.0 C C:THR41 3.4 86.9 1.0 CB C:THR41 3.5 87.4 1.0 C C:GLY44 3.5 94.2 1.0 CA C:THR41 3.8 87.7 1.0 N C:THR41 4.2 83.5 1.0 CG C:GLU55 4.2 71.8 1.0 N C:GLY44 4.3 94.9 1.0 N C:GLY45 4.4 92.6 1.0 CA C:GLY45 4.4 93.6 1.0 OD2 C:ASP47 4.4 85.5 1.0 CB C:ASP39 4.4 81.9 1.0 CA C:GLY44 4.4 95.2 1.0 N C:ILE42 4.5 86.9 1.0 OD1 C:ASN50 4.6 73.9 1.0 CZ C:PHE49 4.7 62.6 1.0 NE2 C:HIS61 4.7 67.4 1.0 CG2 C:THR41 4.8 76.7 1.0 ND2 C:ASN50 4.9 69.0 1.0 CB C:GLU55 4.9 74.9 1.0 CE1 C:PHE49 5.0 65.2 1.0 CA C:ILE42 5.0 85.3 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