Calcium in PDB 5s57: Tubulin-Z2856434883-Complex

The structure of Tubulin-Z2856434883-Complex, PDB code: 5s57 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)	63.38 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.68, 159.27, 180.71, 90, 90, 90
R / Rfree (%)	20.7 / 24.5

The structure of Tubulin-Z2856434883-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z2856434883-Complex (pdb code 5s57). 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-Z2856434883-Complex, PDB code: 5s57:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2856434883-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2856434883-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:126.0 occ:1.00 OD1 A:ASP39 2.3 130.5 1.0 O A:GLY44 2.3 133.2 1.0 OE2 A:GLU55 2.3 123.8 1.0 OG1 A:THR41 2.4 137.0 1.0 OD2 A:ASP39 2.6 127.7 1.0 CG A:ASP39 2.7 125.5 1.0 O A:THR41 2.9 135.1 1.0 OE1 A:GLU55 3.0 127.1 1.0 CD A:GLU55 3.0 124.7 1.0 C A:GLY44 3.4 132.7 1.0 CB A:THR41 3.6 136.4 1.0 CA A:GLY45 3.7 129.0 1.0 OD2 A:ASP47 3.7 122.7 1.0 C A:THR41 3.9 140.0 1.0 N A:GLY45 3.9 128.2 1.0 CZ A:PHE49 3.9 112.2 1.0 OD1 A:ASN50 4.0 120.2 1.0 CA A:THR41 4.2 140.0 1.0 CB A:ASP39 4.2 127.5 1.0 CE1 A:PHE49 4.4 107.0 1.0 N A:THR41 4.4 138.3 1.0 ND2 A:ASN50 4.5 111.5 1.0 CG A:GLU55 4.5 124.7 1.0 C A:GLY45 4.6 128.1 1.0 CA A:GLY44 4.6 135.0 1.0 CG A:ASN50 4.7 112.2 1.0 N A:GLY44 4.7 136.2 1.0 CG A:ASP47 4.8 121.9 1.0 CG2 A:THR41 4.8 128.9 1.0 NE2 A:HIS61 4.9 113.2 1.0 CA A:ASP39 5.0 133.8 1.0 CE2 A:PHE49 5.0 110.0 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2856434883-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2856434883-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:128.5 occ:1.00 OE1 B:GLU113 2.8 91.5 1.0 OE2 B:GLU113 3.4 95.9 1.0 CD B:GLU113 3.5 92.6 1.0 OE1 B:GLU110 4.4 75.9 1.0 CG B:GLU113 4.9 77.6 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2856434883-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2856434883-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:95.1 occ:1.00 O C:GLY44 2.4 120.0 1.0 O C:THR41 2.4 102.9 1.0 OE2 C:GLU55 2.5 91.5 1.0 OG1 C:THR41 2.5 99.8 1.0 O C:HOH602 2.5 84.5 1.0 OE1 C:GLU55 2.5 91.8 1.0 OD2 C:ASP39 2.6 88.7 1.0 OD1 C:ASP39 2.7 94.8 1.0 CD C:GLU55 2.8 92.2 1.0 CG C:ASP39 3.0 91.3 1.0 C C:THR41 3.3 101.7 1.0 CB C:THR41 3.3 100.4 1.0 C C:GLY44 3.5 118.8 1.0 CA C:THR41 3.7 99.2 1.0 N C:THR41 4.2 98.3 1.0 N C:GLY44 4.3 120.3 1.0 N C:ILE42 4.3 102.6 1.0 N C:GLY45 4.3 107.3 1.0 CG C:GLU55 4.3 85.8 1.0 CA C:GLY44 4.4 120.5 1.0 OD2 C:ASP47 4.4 95.0 1.0 CA C:GLY45 4.4 104.4 1.0 CB C:ASP39 4.4 93.3 1.0 CG2 C:THR41 4.7 95.3 1.0 NE2 C:HIS61 4.8 77.4 1.0 OD1 C:ASN50 4.8 84.7 1.0 CA C:ILE42 4.8 100.7 1.0 CZ C:PHE49 4.9 78.3 1.0 ND2 C:ASN50 5.0 85.7 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2856434883-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2856434883-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:114.5 occ:1.00 O A:HOH627 2.7 91.7 1.0 O A:HOH622 2.7 99.3 1.0 OD2 E:ASP44 3.2 125.5 1.0 O A:GLU196 4.1 103.3 1.0 OG A:SER158 4.3 89.3 1.0 CG E:ASP44 4.3 127.5 1.0 CB A:SER158 4.6 87.5 1.0 OD1 E:ASP44 4.7 123.5 1.0 NZ A:LYS166 4.8 88.9 1.0 CA A:HIS197 4.8 96.0 1.0 O A:GLY162 5.0 107.4 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