Calcium in PDB 5s5p: Tubulin-Z53825177-Complex

The structure of Tubulin-Z53825177-Complex, PDB code: 5s5p 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)	80.32 / 2.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.71, 160.63, 179.04, 90, 90, 90
R / Rfree (%)	22.4 / 26.5

The structure of Tubulin-Z53825177-Complex also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Fluorine	(F)	1 atom

The binding sites of Calcium atom in the Tubulin-Z53825177-Complex (pdb code 5s5p). 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-Z53825177-Complex, PDB code: 5s5p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z53825177-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z53825177-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:142.9 occ:1.00 OD2 A:ASP39 2.3 139.8 1.0 OE2 A:GLU55 2.3 140.9 1.0 O A:HOH605 2.3 141.1 1.0 OG1 A:THR41 2.5 151.6 1.0 O A:GLY44 2.5 155.0 1.0 OD1 A:ASP39 2.6 146.3 1.0 O A:THR41 2.6 153.8 1.0 OE1 A:GLU55 2.7 148.3 1.0 CG A:ASP39 2.8 142.7 1.0 CD A:GLU55 2.8 143.1 1.0 CB A:THR41 3.5 152.3 1.0 C A:THR41 3.6 155.2 1.0 C A:GLY44 3.6 154.7 1.0 CA A:THR41 3.9 153.8 1.0 N A:THR41 4.2 151.5 1.0 CB A:ASP39 4.2 141.4 1.0 CZ A:PHE49 4.2 118.0 1.0 CA A:GLY45 4.3 157.7 1.0 CG A:GLU55 4.3 140.4 1.0 N A:GLY45 4.3 157.1 1.0 OD2 A:ASP47 4.4 123.0 1.0 N A:GLY44 4.4 152.1 1.0 OD1 A:ASN50 4.4 131.1 1.0 CA A:GLY44 4.6 151.9 1.0 NE2 A:HIS61 4.7 130.6 1.0 N A:ILE42 4.8 160.9 1.0 CG2 A:THR41 4.8 155.0 1.0 CE2 A:PHE49 4.9 118.1 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z53825177-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z53825177-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:119.9 occ:1.00 OD2 E:ASP44 3.6 142.7 1.0 OG A:SER158 4.1 116.6 1.0 NZ A:LYS166 4.2 108.0 1.0 O A:GLU196 4.2 107.4 1.0 CB A:SER158 4.5 114.0 1.0 O A:GLY162 4.6 149.8 1.0 CG E:ASP44 4.7 143.2 1.0 CA A:HIS197 4.8 105.5 1.0 O A:HIS197 4.8 102.3 1.0 OD1 A:ASP199 4.8 120.3 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z53825177-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z53825177-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:136.2 occ:1.00 OE1 B:GLU113 2.8 113.2 1.0 OE1 B:GLU110 3.7 105.3 1.0 CD B:GLU113 3.8 106.4 1.0 OE2 B:GLU113 4.1 101.3 1.0 CD B:GLU110 4.5 96.1 1.0 OE2 B:GLU110 4.5 97.3 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z53825177-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z53825177-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:96.5 occ:1.00 OE1 C:GLU55 2.3 100.3 1.0 O C:THR41 2.4 112.4 1.0 OE2 C:GLU55 2.4 98.1 1.0 OD2 C:ASP39 2.4 100.0 1.0 O C:GLY44 2.5 106.7 1.0 O C:HOH605 2.6 99.5 1.0 OD1 C:ASP39 2.6 107.2 1.0 OG1 C:THR41 2.6 108.4 1.0 CD C:GLU55 2.7 95.1 1.0 CG C:ASP39 2.8 103.5 1.0 C C:THR41 3.4 112.2 1.0 CB C:THR41 3.4 108.9 1.0 C C:GLY44 3.6 108.3 1.0 CA C:THR41 3.8 113.8 1.0 N C:THR41 4.2 111.8 1.0 CG C:GLU55 4.2 91.7 1.0 CB C:ASP39 4.4 107.3 1.0 N C:GLY44 4.4 111.2 1.0 N C:GLY45 4.5 115.8 1.0 N C:ILE42 4.5 113.0 1.0 OD2 C:ASP47 4.5 103.5 1.0 CA C:GLY45 4.5 115.2 1.0 CA C:GLY44 4.5 110.6 1.0 CZ C:PHE49 4.6 88.6 1.0 NE2 C:HIS61 4.8 91.6 1.0 ND2 C:ASN50 4.8 94.7 1.0 CG2 C:THR41 4.8 104.5 1.0 CE1 C:PHE49 5.0 86.7 1.0 CA C:ILE42 5.0 111.8 1.0 OD1 C:ASN50 5.0 103.0 1.0 CB C:GLU55 5.0 94.2 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