Calcium in PDB 5s4w: Tubulin-Z1416571195-Complex

The structure of Tubulin-Z1416571195-Complex, PDB code: 5s4w 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)	62.66 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.13, 160.08, 178.76, 90, 90, 90
R / Rfree (%)	22.1 / 26.8

The structure of Tubulin-Z1416571195-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1416571195-Complex (pdb code 5s4w). 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-Z1416571195-Complex, PDB code: 5s4w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1416571195-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1416571195-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:134.3 occ:1.00 OE2 A:GLU55 2.3 131.4 1.0 O A:THR41 2.4 139.9 1.0 OE1 A:GLU55 2.4 138.2 1.0 O A:HOH606 2.5 134.9 1.0 OG1 A:THR41 2.5 139.1 1.0 O A:GLY44 2.6 153.4 1.0 OD1 A:ASP39 2.7 133.4 1.0 OD2 A:ASP39 2.7 132.6 1.0 CD A:GLU55 2.7 134.3 1.0 CG A:ASP39 3.0 132.1 1.0 C A:THR41 3.5 141.5 1.0 CB A:THR41 3.5 139.0 1.0 C A:GLY44 3.6 151.4 1.0 CA A:THR41 3.9 138.4 1.0 CG A:GLU55 4.2 130.1 1.0 N A:THR41 4.3 133.8 1.0 OD1 A:ASN50 4.3 127.8 1.0 CA A:GLY45 4.3 148.0 1.0 CZ A:PHE49 4.3 112.2 1.0 OD2 A:ASP47 4.3 120.9 1.0 N A:GLY45 4.4 147.7 1.0 N A:GLY44 4.5 150.2 1.0 CB A:ASP39 4.6 129.9 1.0 N A:ILE42 4.6 143.8 1.0 CA A:GLY44 4.6 147.9 1.0 CG2 A:THR41 4.8 143.3 1.0 ND2 A:ASN50 4.8 122.8 1.0 CE1 A:PHE49 4.9 114.2 1.0 NE2 A:HIS61 4.9 126.3 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1416571195-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1416571195-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:129.3 occ:1.00 O E:HOH201 2.6 109.5 1.0 OG A:SER158 4.1 107.6 1.0 NZ A:LYS166 4.1 107.3 1.0 OD2 E:ASP44 4.1 137.1 1.0 O A:GLU196 4.3 110.3 1.0 CB A:SER158 4.4 110.1 1.0 O A:GLY162 4.5 144.9 1.0 O A:HIS197 4.6 102.7 1.0 CA A:HIS197 4.7 107.4 1.0 CE A:LYS166 4.8 103.4 1.0 C A:HIS197 4.9 103.4 1.0 OD1 A:ASP199 4.9 118.0 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1416571195-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1416571195-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:129.4 occ:1.00 OE1 B:GLU113 2.6 116.9 1.0 CD B:GLU113 3.6 110.6 1.0 OE2 B:GLU113 3.8 103.8 1.0 OE1 B:GLU110 4.0 98.6 1.0 CD B:GLU110 4.9 97.9 1.0 OE2 B:GLU110 4.9 97.3 1.0 CG B:GLU113 5.0 97.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1416571195-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1416571195-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:104.5 occ:1.00 O C:THR41 2.2 118.3 1.0 OE1 C:GLU55 2.3 115.3 1.0 OE2 C:GLU55 2.4 99.7 1.0 OD2 C:ASP39 2.4 108.4 1.0 O C:GLY44 2.4 131.9 1.0 OG1 C:THR41 2.4 113.2 1.0 O C:HOH603 2.5 106.2 1.0 OD1 C:ASP39 2.5 112.8 1.0 CD C:GLU55 2.7 106.2 1.0 CG C:ASP39 2.8 111.9 1.0 C C:THR41 3.3 118.3 1.0 CB C:THR41 3.4 117.8 1.0 C C:GLY44 3.6 131.6 1.0 CA C:THR41 3.8 122.4 1.0 N C:THR41 4.1 120.2 1.0 CG C:GLU55 4.2 99.7 1.0 OD2 C:ASP47 4.3 110.6 1.0 CB C:ASP39 4.3 116.1 1.0 N C:GLY44 4.4 133.2 1.0 N C:ILE42 4.4 119.7 1.0 N C:GLY45 4.5 133.9 1.0 CA C:GLY45 4.5 126.3 1.0 CZ C:PHE49 4.6 93.2 1.0 CA C:GLY44 4.6 131.0 1.0 NE2 C:HIS61 4.7 103.5 1.0 CG2 C:THR41 4.8 115.2 1.0 OD1 C:ASN50 4.8 102.3 1.0 CA C:ILE42 4.8 122.2 1.0 CE1 C:PHE49 4.9 96.9 1.0 CB C:GLU55 4.9 103.7 1.0 ND2 C:ASN50 5.0 94.6 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