Calcium in PDB 5s5n: Tubulin-Z165170770-Complex

The structure of Tubulin-Z165170770-Complex, PDB code: 5s5n 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)	63.62 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.61, 159.43, 179.48, 90, 90, 90
R / Rfree (%)	22.2 / 27.4

The structure of Tubulin-Z165170770-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z165170770-Complex (pdb code 5s5n). 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-Z165170770-Complex, PDB code: 5s5n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z165170770-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z165170770-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:117.4 occ:1.00 OE2 A:GLU55 2.4 122.5 1.0 OD2 A:ASP39 2.4 113.5 1.0 OG1 A:THR41 2.4 119.3 1.0 O A:GLY44 2.4 119.2 1.0 OE1 A:GLU55 2.4 126.5 1.0 OD1 A:ASP39 2.5 111.2 1.0 O A:THR41 2.7 115.9 1.0 CD A:GLU55 2.7 123.4 1.0 CG A:ASP39 2.7 112.8 1.0 CB A:THR41 3.5 117.0 1.0 C A:GLY44 3.6 121.0 1.0 C A:THR41 3.6 116.8 1.0 OD2 A:ASP47 3.9 109.3 1.0 CA A:THR41 4.0 117.7 1.0 CZ A:PHE49 4.1 95.1 1.0 CG A:GLU55 4.2 122.2 1.0 CB A:ASP39 4.2 111.5 1.0 CA A:GLY45 4.3 133.7 1.0 N A:THR41 4.3 116.2 1.0 N A:GLY45 4.4 130.4 1.0 OD1 A:ASN50 4.4 106.8 1.0 N A:GLY44 4.4 117.5 1.0 ND2 A:ASN50 4.5 110.2 1.0 CA A:GLY44 4.6 116.5 1.0 CE2 A:PHE49 4.6 96.7 1.0 CG2 A:THR41 4.7 118.1 1.0 N A:ILE42 4.8 118.5 1.0 NE2 A:HIS61 4.8 110.5 1.0 CG A:ASN50 4.9 103.7 1.0 O A:GLY45 4.9 132.5 1.0 C A:GLY45 5.0 136.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z165170770-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z165170770-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:122.7 occ:1.00 OE1 B:GLU113 2.9 117.2 1.0 CD B:GLU113 3.8 114.3 1.0 OE2 B:GLU113 3.8 108.5 1.0 OE1 B:GLU110 4.0 87.4 1.0 OE2 B:GLU110 4.8 87.4 1.0 CD B:GLU110 4.8 84.4 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z165170770-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z165170770-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:101.2 occ:1.00 OD2 C:ASP39 2.3 92.4 1.0 OE2 C:GLU55 2.4 86.7 1.0 OG1 C:THR41 2.5 105.8 1.0 O C:THR41 2.5 100.2 1.0 OE1 C:GLU55 2.5 101.8 1.0 O C:GLY44 2.6 124.6 1.0 OD1 C:ASP39 2.6 99.8 1.0 CD C:GLU55 2.8 90.5 1.0 CG C:ASP39 2.8 94.3 1.0 CB C:THR41 3.2 104.6 1.0 C C:GLY44 3.4 123.8 1.0 C C:THR41 3.4 100.1 1.0 CA C:THR41 3.8 100.6 1.0 OD2 C:ASP47 3.9 93.3 1.0 CA C:GLY45 4.0 105.8 1.0 N C:GLY45 4.1 108.5 1.0 N C:THR41 4.1 103.9 1.0 OD1 C:ASN50 4.2 81.7 1.0 CG C:GLU55 4.3 87.9 1.0 CB C:ASP39 4.3 95.9 1.0 N C:GLY44 4.4 122.7 1.0 CA C:GLY44 4.4 122.6 1.0 CZ C:PHE49 4.5 81.1 1.0 N C:ILE42 4.6 100.8 1.0 CG2 C:THR41 4.6 103.5 1.0 CE1 C:PHE49 4.6 77.3 1.0 ND2 C:ASN50 4.6 88.1 1.0 NE2 C:HIS61 4.7 89.8 1.0 CG C:ASN50 4.9 84.6 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z165170770-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z165170770-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:97.3 occ:1.00 O A:HOH609 2.8 87.2 1.0 OD2 E:ASP44 3.3 143.8 1.0 OG A:SER158 3.9 90.0 1.0 O A:GLU196 4.0 95.6 1.0 NZ A:LYS166 4.2 88.7 1.0 CB A:SER158 4.3 93.7 1.0 CG E:ASP44 4.3 143.7 1.0 OD1 E:ASP44 4.6 143.0 1.0 O A:GLY162 4.6 138.7 1.0 CA A:HIS197 4.7 90.2 1.0 ND1 A:HIS197 4.9 94.0 1.0 CE A:LYS166 4.9 90.5 1.0 O A:HIS197 4.9 89.8 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