Calcium in PDB 5s5u: Tubulin-Z1124201124-Complex

The structure of Tubulin-Z1124201124-Complex, PDB code: 5s5u 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)	79.33 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.78, 158.65, 178.88, 90, 90, 90
R / Rfree (%)	21 / 25.6

The structure of Tubulin-Z1124201124-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1124201124-Complex (pdb code 5s5u). 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-Z1124201124-Complex, PDB code: 5s5u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1124201124-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1124201124-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:105.4 occ:1.00 O A:GLY44 2.3 109.0 1.0 O A:HOH617 2.3 99.4 1.0 OD1 A:ASP39 2.3 102.2 1.0 OE2 A:GLU55 2.3 103.0 1.0 OD2 A:ASP39 2.4 98.8 1.0 OG1 A:THR41 2.4 107.7 1.0 O A:THR41 2.6 106.9 1.0 CG A:ASP39 2.7 103.7 1.0 OE1 A:GLU55 2.8 99.1 1.0 CD A:GLU55 2.9 101.1 1.0 C A:GLY44 3.5 110.2 1.0 CB A:THR41 3.5 105.4 1.0 C A:THR41 3.6 107.2 1.0 CA A:THR41 4.0 107.6 1.0 O A:HOH602 4.0 101.1 1.0 CB A:ASP39 4.2 102.9 1.0 CA A:GLY45 4.2 111.2 1.0 CZ A:PHE49 4.2 92.2 1.0 N A:THR41 4.3 106.5 1.0 N A:GLY45 4.3 107.9 1.0 OD1 A:ASN50 4.3 101.4 1.0 N A:GLY44 4.3 110.1 1.0 CG A:GLU55 4.4 95.5 1.0 OD2 A:ASP47 4.5 99.0 1.0 CA A:GLY44 4.5 110.5 1.0 NE2 A:HIS61 4.7 96.1 1.0 N A:ILE42 4.8 107.1 1.0 CG2 A:THR41 4.8 100.8 1.0 CE1 A:PHE49 4.8 90.2 1.0 ND2 A:ASN50 4.8 90.2 1.0 CA A:ASP39 4.9 105.7 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1124201124-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1124201124-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:105.4 occ:1.00 OE1 B:GLU113 2.5 92.3 1.0 OE2 B:GLU113 3.2 86.9 1.0 CD B:GLU113 3.2 91.5 1.0 CG B:GLU113 4.7 82.9 1.0 OE1 B:GLU110 4.8 63.5 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1124201124-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1124201124-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:83.9 occ:1.00 O C:THR41 2.3 88.1 1.0 O C:GLY44 2.3 88.6 1.0 OG1 C:THR41 2.4 91.7 1.0 OD2 C:ASP39 2.4 80.4 1.0 O C:HOH605 2.4 79.2 1.0 OE1 C:GLU55 2.5 86.1 1.0 OE2 C:GLU55 2.5 77.2 1.0 OD1 C:ASP39 2.6 82.9 1.0 CG C:ASP39 2.8 82.9 1.0 CD C:GLU55 2.8 76.3 1.0 C C:THR41 3.3 89.2 1.0 CB C:THR41 3.4 86.8 1.0 C C:GLY44 3.5 91.4 1.0 CA C:THR41 3.8 89.2 1.0 N C:THR41 4.0 88.7 1.0 CB C:ASP39 4.3 86.0 1.0 CG C:GLU55 4.3 75.0 1.0 CA C:GLY45 4.4 93.4 1.0 N C:GLY45 4.4 94.5 1.0 OD2 C:ASP47 4.4 84.9 1.0 N C:GLY44 4.4 95.3 1.0 CA C:GLY44 4.5 94.5 1.0 N C:ILE42 4.5 89.4 1.0 CZ C:PHE49 4.6 70.5 1.0 OD1 C:ASN50 4.6 76.7 1.0 CG2 C:THR41 4.7 78.2 1.0 NE2 C:HIS61 4.8 74.9 1.0 CA C:ILE42 5.0 85.7 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1124201124-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1124201124-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:107.2 occ:1.00 OD2 E:ASP44 3.3 122.9 1.0 O A:HOH636 3.4 83.6 1.0 O A:HOH623 3.4 78.0 1.0 OG A:SER158 3.8 84.1 1.0 O A:GLU196 4.2 90.2 1.0 NZ A:LYS166 4.2 75.3 1.0 CB A:SER158 4.3 80.2 1.0 CG E:ASP44 4.4 122.8 1.0 CA A:HIS197 4.6 84.1 1.0 O A:HIS197 4.6 80.0 1.0 O A:GLY162 4.8 108.6 1.0 C A:HIS197 4.8 81.7 1.0 OD1 E:ASP44 4.9 119.9 1.0 ND1 A:HIS197 5.0 89.5 1.0 CA A:SER158 5.0 83.8 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