Calcium in PDB 5s50: Tubulin-Z57299526-Complex

The structure of Tubulin-Z57299526-Complex, PDB code: 5s50 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)	79.01 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.03, 158.02, 180.88, 90, 90, 90
R / Rfree (%)	20.8 / 27

The structure of Tubulin-Z57299526-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z57299526-Complex (pdb code 5s50). 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-Z57299526-Complex, PDB code: 5s50:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z57299526-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z57299526-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:173.9 occ:1.00 OE2 A:GLU55 2.3 163.1 1.0 OG1 A:THR41 2.4 183.4 1.0 OD1 A:ASP39 2.4 165.0 1.0 O A:HOH602 2.5 163.9 1.0 O A:THR41 2.5 175.8 1.0 OD2 A:ASP39 2.5 164.9 1.0 O A:GLY44 2.6 186.7 1.0 OE1 A:GLU55 2.7 168.7 1.0 CG A:ASP39 2.8 162.6 1.0 CD A:GLU55 2.8 161.6 1.0 CB A:THR41 3.4 183.1 1.0 C A:THR41 3.5 179.7 1.0 C A:GLY44 3.6 185.4 1.0 CA A:THR41 3.9 178.3 1.0 CA A:GLY45 4.1 178.4 1.0 OD2 A:ASP47 4.2 155.8 1.0 CZ A:PHE49 4.2 137.8 1.0 N A:THR41 4.2 178.0 1.0 N A:GLY45 4.2 181.7 1.0 CB A:ASP39 4.2 156.1 1.0 CG A:GLU55 4.3 151.8 1.0 OD1 A:ASN50 4.4 159.2 1.0 N A:GLY44 4.5 188.4 1.0 CA A:GLY44 4.6 188.2 1.0 N A:ILE42 4.7 182.1 1.0 CG2 A:THR41 4.7 177.6 1.0 CE1 A:PHE49 4.8 134.5 1.0 NE2 A:HIS61 4.8 151.3 1.0 ND2 A:ASN50 4.9 132.7 1.0 C A:GLY45 5.0 181.7 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z57299526-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z57299526-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:154.5 occ:1.00 O E:HOH201 2.5 119.9 1.0 NZ A:LYS166 3.7 127.5 1.0 O A:GLY162 3.9 172.8 1.0 OG A:SER158 4.1 126.7 1.0 OD1 A:ASP199 4.3 136.3 1.0 O A:LYS164 4.4 160.9 1.0 OD2 E:ASP44 4.5 165.2 1.0 CB A:SER158 4.6 132.6 1.0 O A:HIS197 4.8 122.4 1.0 OD2 A:ASP199 4.8 137.4 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z57299526-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z57299526-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:135.6 occ:1.00 OE1 B:GLU113 2.9 138.8 1.0 OE1 B:GLU110 3.8 118.2 1.0 CD B:GLU113 3.9 144.8 1.0 OE2 B:GLU113 4.1 143.0 1.0 CD B:GLU110 4.6 114.1 1.0 OE2 B:GLU110 4.7 128.1 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z57299526-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z57299526-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:122.2 occ:1.00 OE2 C:GLU55 2.2 122.5 1.0 OG1 C:THR41 2.3 138.6 1.0 OD2 C:ASP39 2.3 130.0 1.0 OD1 C:ASP39 2.4 126.7 1.0 O C:HOH601 2.4 130.0 1.0 O C:GLY44 2.5 174.3 1.0 O C:THR41 2.6 146.8 1.0 CG C:ASP39 2.7 128.8 1.0 CD C:GLU55 2.9 132.6 1.0 OE1 C:GLU55 2.9 140.5 1.0 CB C:THR41 3.3 143.0 1.0 C C:THR41 3.5 151.5 1.0 C C:GLY44 3.7 173.6 1.0 CA C:THR41 3.8 145.3 1.0 N C:THR41 4.0 142.4 1.0 OD2 C:ASP47 4.1 132.1 1.0 CB C:ASP39 4.2 128.0 1.0 CA C:GLY45 4.3 144.2 1.0 CG C:GLU55 4.4 127.1 1.0 CZ C:PHE49 4.4 112.9 1.0 N C:GLY45 4.5 151.0 1.0 OD1 C:ASN50 4.5 121.1 1.0 CG2 C:THR41 4.6 139.3 1.0 N C:GLY44 4.6 175.5 1.0 N C:ILE42 4.7 151.3 1.0 CA C:GLY44 4.8 175.8 1.0 CE1 C:PHE49 4.8 111.7 1.0 ND2 C:ASN50 4.8 118.6 1.0 NE2 C:HIS61 4.9 119.1 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