Calcium in PDB 5s56: Tubulin-Z2856434783-Complex

The structure of Tubulin-Z2856434783-Complex, PDB code: 5s56 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 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.56, 158.3, 180.09, 90, 90, 90
R / Rfree (%)	20.4 / 23.9

The structure of Tubulin-Z2856434783-Complex also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Fluorine	(F)	2 atoms

The binding sites of Calcium atom in the Tubulin-Z2856434783-Complex (pdb code 5s56). 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-Z2856434783-Complex, PDB code: 5s56:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2856434783-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2856434783-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:102.7 occ:1.00 O A:GLY44 2.3 106.0 1.0 OE2 A:GLU55 2.4 100.9 1.0 OD2 A:ASP39 2.4 102.3 1.0 OG1 A:THR41 2.6 108.4 1.0 OD1 A:ASP39 2.6 111.8 1.0 O A:THR41 2.7 112.6 1.0 OE1 A:GLU55 2.8 103.6 1.0 CG A:ASP39 2.8 106.6 1.0 CD A:GLU55 2.9 102.7 1.0 C A:GLY44 3.3 108.8 1.0 CB A:THR41 3.7 112.4 1.0 C A:THR41 3.8 113.8 1.0 CA A:GLY45 3.8 113.7 1.0 N A:GLY45 4.0 109.4 1.0 OD2 A:ASP47 4.0 108.1 1.0 OD1 A:ASN50 4.1 104.3 1.0 CA A:THR41 4.2 114.7 1.0 CZ A:PHE49 4.2 93.1 1.0 CB A:ASP39 4.3 104.5 1.0 CG A:GLU55 4.4 102.5 1.0 ND2 A:ASN50 4.4 91.9 1.0 CA A:GLY44 4.5 111.0 1.0 N A:THR41 4.5 115.3 1.0 N A:GLY44 4.5 111.4 1.0 C A:GLY45 4.7 111.1 1.0 CE1 A:PHE49 4.7 90.5 1.0 CG A:ASN50 4.7 95.5 1.0 NE2 A:HIS61 4.9 98.4 1.0 CG2 A:THR41 4.9 104.6 1.0 N A:ILE42 4.9 114.8 1.0 CG A:ASP47 4.9 106.3 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2856434783-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2856434783-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:99.9 occ:1.00 O A:HOH643 2.7 79.8 1.0 O A:HOH622 2.7 88.7 1.0 OD2 E:ASP44 3.5 110.8 1.0 O A:HOH620 3.6 69.6 1.0 O A:HOH641 3.8 86.7 1.0 OG A:SER158 4.0 80.8 1.0 O A:GLU196 4.2 78.8 1.0 NZ A:LYS166 4.4 70.5 1.0 CB A:SER158 4.5 74.6 1.0 CG E:ASP44 4.7 111.5 1.0 O A:GLY162 4.8 101.5 1.0 CA A:HIS197 4.8 77.5 1.0 O A:HIS197 4.9 75.4 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2856434783-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2856434783-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:115.4 occ:1.00 OE1 B:GLU113 2.5 89.6 1.0 CD B:GLU113 3.5 88.9 1.0 OE2 B:GLU113 3.6 95.0 1.0 OE1 B:GLU110 4.4 66.2 1.0 CG B:GLU113 4.8 79.7 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2856434783-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2856434783-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:82.7 occ:1.00 O C:GLY44 2.3 95.9 1.0 OD1 C:ASP39 2.4 82.6 1.0 OE2 C:GLU55 2.5 79.3 1.0 O C:HOH604 2.5 73.9 1.0 OD2 C:ASP39 2.5 74.0 1.0 O C:THR41 2.5 88.3 1.0 OG1 C:THR41 2.6 83.8 1.0 OE1 C:GLU55 2.6 81.2 1.0 CG C:ASP39 2.8 79.8 1.0 CD C:GLU55 2.9 76.5 1.0 C C:THR41 3.5 89.5 1.0 C C:GLY44 3.5 96.0 1.0 CB C:THR41 3.5 88.0 1.0 CA C:THR41 3.9 89.5 1.0 CA C:GLY45 4.1 88.7 1.0 OD2 C:ASP47 4.2 84.7 1.0 N C:THR41 4.3 91.4 1.0 N C:GLY45 4.3 92.5 1.0 CB C:ASP39 4.3 84.8 1.0 CG C:GLU55 4.4 74.8 1.0 N C:GLY44 4.5 101.0 1.0 CZ C:PHE49 4.6 68.8 1.0 CA C:GLY44 4.6 99.3 1.0 N C:ILE42 4.6 87.6 1.0 OD1 C:ASN50 4.6 69.7 1.0 NE2 C:HIS61 4.7 71.2 1.0 CG2 C:THR41 4.9 73.7 1.0 ND2 C:ASN50 4.9 68.2 1.0 CE1 C:PHE49 5.0 68.0 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