Calcium in PDB 5s4n: Tubulin-Z285782452-Complex

The structure of Tubulin-Z285782452-Complex, PDB code: 5s4n 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)	90.81 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.26, 158.63, 179.55, 90, 90, 90
R / Rfree (%)	21.6 / 25.8

The structure of Tubulin-Z285782452-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z285782452-Complex (pdb code 5s4n). 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-Z285782452-Complex, PDB code: 5s4n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z285782452-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z285782452-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:110.0 occ:1.00 OD2 A:ASP39 2.3 108.1 1.0 O A:HOH620 2.3 110.7 1.0 OG1 A:THR41 2.3 116.0 1.0 OD1 A:ASP39 2.4 110.0 1.0 O A:THR41 2.4 115.2 1.0 OE2 A:GLU55 2.5 105.1 1.0 OE1 A:GLU55 2.6 109.0 1.0 CG A:ASP39 2.7 110.3 1.0 O A:GLY44 2.7 114.6 1.0 CD A:GLU55 2.9 104.5 1.0 CB A:THR41 3.3 117.8 1.0 C A:THR41 3.4 118.6 1.0 CA A:THR41 3.7 118.3 1.0 C A:GLY44 3.8 116.7 1.0 N A:THR41 4.0 114.6 1.0 CB A:ASP39 4.2 109.3 1.0 CZ A:PHE49 4.3 96.1 1.0 OD2 A:ASP47 4.4 107.3 1.0 CG A:GLU55 4.4 101.4 1.0 N A:GLY44 4.4 116.3 1.0 NE2 A:HIS61 4.5 103.0 1.0 CA A:GLY45 4.5 123.1 1.0 N A:ILE42 4.5 122.5 1.0 N A:GLY45 4.6 120.5 1.0 CG2 A:THR41 4.6 113.1 1.0 OD1 A:ASN50 4.7 106.2 1.0 CA A:GLY44 4.7 116.2 1.0 CE2 A:PHE49 4.9 91.6 1.0 ND2 A:ASN50 4.9 101.8 1.0 CA A:ASP39 5.0 112.9 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z285782452-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z285782452-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:133.0 occ:1.00 OE1 B:GLU113 2.8 100.0 1.0 CD B:GLU113 3.7 95.3 1.0 OE2 B:GLU113 3.8 97.8 1.0 OE1 B:GLU110 4.1 73.1 1.0 CD B:GLU110 4.9 71.6 1.0 OE2 B:GLU110 5.0 69.2 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z285782452-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z285782452-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:92.1 occ:1.00 OG1 C:THR41 2.3 103.8 1.0 O C:GLY44 2.4 102.1 1.0 O C:THR41 2.4 103.3 1.0 OE1 C:GLU55 2.4 90.7 1.0 OD2 C:ASP39 2.4 89.9 1.0 OD1 C:ASP39 2.5 95.8 1.0 OE2 C:GLU55 2.5 85.3 1.0 O C:HOH603 2.6 85.5 1.0 CG C:ASP39 2.8 93.3 1.0 CD C:GLU55 2.8 89.0 1.0 CB C:THR41 3.3 104.3 1.0 C C:THR41 3.3 105.2 1.0 C C:GLY44 3.5 102.1 1.0 CA C:THR41 3.8 107.7 1.0 N C:THR41 4.1 104.9 1.0 CA C:GLY45 4.2 98.8 1.0 N C:GLY45 4.3 100.1 1.0 CB C:ASP39 4.3 94.3 1.0 CG C:GLU55 4.4 83.5 1.0 N C:GLY44 4.4 106.1 1.0 OD2 C:ASP47 4.5 92.5 1.0 N C:ILE42 4.5 105.2 1.0 CZ C:PHE49 4.6 75.4 1.0 CA C:GLY44 4.6 104.0 1.0 CG2 C:THR41 4.7 105.6 1.0 OD1 C:ASN50 4.7 80.7 1.0 NE2 C:HIS61 4.8 83.7 1.0 ND2 C:ASN50 4.9 76.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z285782452-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z285782452-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:101.0 occ:1.00 O E:HOH303 2.6 98.0 1.0 OD2 E:ASP44 3.1 115.0 1.0 OG A:SER158 3.8 80.0 1.0 O A:GLU196 4.1 89.0 1.0 CB A:SER158 4.2 85.0 1.0 CG E:ASP44 4.3 116.2 1.0 NZ A:LYS166 4.4 75.5 1.0 O A:GLY162 4.7 122.3 1.0 CA A:HIS197 4.7 81.1 1.0 OD1 E:ASP44 4.7 115.0 1.0 O A:HIS197 4.9 79.9 1.0 ND1 A:HIS197 4.9 82.7 1.0 CA A:SER158 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