Calcium in PDB 5s4y: Tubulin-Z2856434857-Complex

The structure of Tubulin-Z2856434857-Complex, PDB code: 5s4y 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)	78.89 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.14, 157.78, 178.7, 90, 90, 90
R / Rfree (%)	20 / 23.8

The structure of Tubulin-Z2856434857-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z2856434857-Complex (pdb code 5s4y). 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-Z2856434857-Complex, PDB code: 5s4y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2856434857-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2856434857-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:108.7 occ:1.00 O A:GLY44 2.3 119.9 1.0 OD2 A:ASP39 2.3 101.4 1.0 OD1 A:ASP39 2.3 112.5 1.0 OE2 A:GLU55 2.4 105.1 1.0 O A:HOH618 2.4 99.0 1.0 O A:THR41 2.5 118.3 1.0 CG A:ASP39 2.7 106.1 1.0 OE1 A:GLU55 2.7 111.2 1.0 OG1 A:THR41 2.7 105.5 1.0 CD A:GLU55 2.9 106.0 1.0 C A:GLY44 3.5 119.0 1.0 C A:THR41 3.5 121.6 1.0 CB A:THR41 3.6 111.7 1.0 CA A:THR41 4.0 117.2 1.0 CA A:GLY45 4.1 120.7 1.0 CB A:ASP39 4.2 105.7 1.0 N A:GLY45 4.2 116.6 1.0 N A:THR41 4.2 119.5 1.0 CG A:GLU55 4.3 102.3 1.0 CZ A:PHE49 4.4 93.0 1.0 N A:GLY44 4.5 125.2 1.0 OD2 A:ASP47 4.6 104.0 1.0 CA A:GLY44 4.6 123.7 1.0 NE2 A:HIS61 4.6 97.2 1.0 OD1 A:ASN50 4.6 105.5 1.0 N A:ILE42 4.7 120.0 1.0 ND2 A:ASN50 4.9 91.4 1.0 CE1 A:PHE49 4.9 90.6 1.0 CA A:ASP39 5.0 109.6 1.0 CG2 A:THR41 5.0 102.2 1.0 C A:GLY45 5.0 115.5 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2856434857-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2856434857-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:104.8 occ:1.00 O E:HOH201 2.6 89.3 1.0 O A:HOH642 3.0 77.9 1.0 OG A:SER158 3.9 80.1 1.0 O A:HOH636 4.0 84.8 1.0 NZ A:LYS166 4.0 72.4 1.0 OD2 E:ASP44 4.3 108.3 1.0 O A:GLY162 4.3 111.4 1.0 CB A:SER158 4.5 75.8 1.0 O A:HIS197 4.5 73.8 1.0 O A:GLU196 4.5 80.3 1.0 OD1 A:ASP199 4.8 84.9 1.0 CA A:HIS197 4.8 78.3 1.0 OD2 A:ASP199 4.8 84.3 1.0 O A:LYS164 4.9 90.1 1.0 C A:HIS197 4.9 76.4 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2856434857-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2856434857-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:114.4 occ:1.00 OE1 B:GLU113 2.4 95.8 1.0 CD B:GLU113 3.3 99.5 1.0 OE2 B:GLU113 3.4 97.8 1.0 OE1 B:GLU110 4.0 73.5 1.0 CG B:GLU113 4.7 85.8 1.0 CD B:GLU110 4.7 76.2 1.0 OE2 B:GLU110 4.7 87.1 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2856434857-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2856434857-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:90.4 occ:1.00 OD2 C:ASP39 2.3 86.1 1.0 O C:HOH601 2.3 84.2 1.0 OE2 C:GLU55 2.4 90.7 1.0 OG1 C:THR41 2.5 97.2 1.0 O C:THR41 2.5 94.6 1.0 O C:GLY44 2.5 98.0 1.0 OE1 C:GLU55 2.6 96.4 1.0 OD1 C:ASP39 2.7 86.5 1.0 CD C:GLU55 2.8 83.6 1.0 CG C:ASP39 2.8 90.7 1.0 C C:THR41 3.4 101.6 1.0 CB C:THR41 3.5 99.0 1.0 C C:GLY44 3.7 99.2 1.0 CA C:THR41 3.9 95.7 1.0 OD2 C:ASP47 4.1 90.6 1.0 N C:THR41 4.3 100.7 1.0 CG C:GLU55 4.3 83.1 1.0 CB C:ASP39 4.3 93.9 1.0 CA C:GLY45 4.4 103.3 1.0 N C:ILE42 4.5 101.6 1.0 N C:GLY45 4.5 102.6 1.0 CZ C:PHE49 4.5 79.0 1.0 N C:GLY44 4.5 104.8 1.0 NE2 C:HIS61 4.6 82.1 1.0 CA C:GLY44 4.6 104.5 1.0 CG2 C:THR41 4.8 86.7 1.0 OD1 C:ASN50 4.8 84.2 1.0 ND2 C:ASN50 4.8 75.1 1.0 CA C:ILE42 4.9 97.0 1.0 CE1 C:PHE49 4.9 81.1 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