Calcium in PDB 5s5a: Tubulin-Z1449748885-Complex

The structure of Tubulin-Z1449748885-Complex, PDB code: 5s5a 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)	63.08 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.59, 158.16, 179.51, 90, 90, 90
R / Rfree (%)	20.6 / 23.7

The structure of Tubulin-Z1449748885-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1449748885-Complex (pdb code 5s5a). 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-Z1449748885-Complex, PDB code: 5s5a:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1449748885-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1449748885-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:94.3 occ:1.00 O A:GLY44 2.3 98.0 1.0 OD2 A:ASP39 2.4 87.4 1.0 OE2 A:GLU55 2.4 88.8 1.0 OD1 A:ASP39 2.4 96.1 1.0 OG1 A:THR41 2.6 94.4 1.0 CG A:ASP39 2.7 90.6 1.0 O A:THR41 2.7 102.4 1.0 OE1 A:GLU55 2.8 93.2 1.0 CD A:GLU55 2.9 91.5 1.0 C A:GLY44 3.4 97.6 1.0 CB A:THR41 3.5 96.1 1.0 C A:THR41 3.7 104.1 1.0 CA A:GLY45 3.9 102.4 1.0 CA A:THR41 4.0 102.7 1.0 N A:GLY45 4.1 97.7 1.0 CZ A:PHE49 4.1 83.0 1.0 OD2 A:ASP47 4.2 92.8 1.0 CB A:ASP39 4.2 92.8 1.0 OD1 A:ASN50 4.3 90.3 1.0 N A:THR41 4.3 102.6 1.0 CG A:GLU55 4.4 86.7 1.0 N A:GLY44 4.5 103.6 1.0 CA A:GLY44 4.5 100.7 1.0 ND2 A:ASN50 4.7 83.1 1.0 NE2 A:HIS61 4.8 87.6 1.0 CE2 A:PHE49 4.8 83.1 1.0 CG2 A:THR41 4.9 86.7 1.0 C A:GLY45 4.9 96.8 1.0 CE1 A:PHE49 4.9 81.1 1.0 N A:ILE42 4.9 111.7 1.0 CG A:ASN50 4.9 85.2 1.0 CA A:ASP39 5.0 98.4 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1449748885-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1449748885-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:96.9 occ:1.00 O E:HOH306 2.5 86.4 1.0 O A:HOH651 2.6 82.7 1.0 O A:HOH622 3.6 67.3 1.0 OD2 E:ASP44 3.8 98.0 1.0 O A:HOH654 3.9 85.6 1.0 OG A:SER158 4.1 69.4 1.0 O A:GLU196 4.3 80.1 1.0 NZ A:LYS166 4.4 62.8 1.0 CB A:SER158 4.6 67.4 1.0 OD1 A:ASP199 4.6 76.9 1.0 O A:GLY162 4.8 96.6 1.0 O A:HIS197 4.8 67.9 1.0 CA A:HIS197 4.8 73.3 1.0 CG E:ASP44 4.9 97.0 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1449748885-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1449748885-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:96.7 occ:1.00 OE1 B:GLU113 2.2 83.4 1.0 CD B:GLU113 3.2 84.4 1.0 OE2 B:GLU113 3.3 77.8 1.0 OE1 B:GLU110 4.1 68.8 1.0 CG B:GLU113 4.6 67.6 1.0 CB B:GLU113 4.9 66.0 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1449748885-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1449748885-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:70.3 occ:1.00 O C:GLY44 2.4 67.0 1.0 OE2 C:GLU55 2.4 64.5 1.0 O C:THR41 2.4 71.4 1.0 OE1 C:GLU55 2.5 68.8 1.0 O C:HOH603 2.5 61.7 1.0 OD1 C:ASP39 2.5 64.3 1.0 OG1 C:THR41 2.5 72.6 1.0 OD2 C:ASP39 2.6 66.5 1.0 CD C:GLU55 2.8 66.2 1.0 CG C:ASP39 2.9 65.4 1.0 C C:THR41 3.4 75.1 1.0 CB C:THR41 3.4 75.8 1.0 C C:GLY44 3.5 71.1 1.0 CA C:THR41 3.8 76.0 1.0 CA C:GLY45 4.1 76.2 1.0 N C:THR41 4.2 76.4 1.0 N C:GLY45 4.2 76.5 1.0 CG C:GLU55 4.3 63.7 1.0 OD2 C:ASP47 4.3 69.8 1.0 CB C:ASP39 4.4 69.6 1.0 N C:GLY44 4.5 70.9 1.0 N C:ILE42 4.5 73.2 1.0 CA C:GLY44 4.5 72.6 1.0 CZ C:PHE49 4.6 61.8 1.0 OD1 C:ASN50 4.6 63.4 1.0 CG2 C:THR41 4.8 67.2 1.0 NE2 C:HIS61 4.8 66.3 1.0 ND2 C:ASN50 4.9 61.1 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