Calcium in PDB 5s5k: Tubulin-Z2472938267-Complex

The structure of Tubulin-Z2472938267-Complex, PDB code: 5s5k 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)	73.28 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.46, 160.78, 178.27, 90, 90, 90
R / Rfree (%)	21.4 / 24.8

The structure of Tubulin-Z2472938267-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z2472938267-Complex (pdb code 5s5k). 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-Z2472938267-Complex, PDB code: 5s5k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2472938267-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2472938267-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:111.1 occ:1.00 O A:GLY44 2.3 112.2 1.0 OE2 A:GLU55 2.3 104.8 1.0 OG1 A:THR41 2.4 110.5 1.0 OD1 A:ASP39 2.5 111.3 1.0 OD2 A:ASP39 2.5 105.0 1.0 O A:THR41 2.8 115.2 1.0 CG A:ASP39 2.8 108.1 1.0 CD A:GLU55 3.1 105.1 1.0 OE1 A:GLU55 3.2 109.7 1.0 CB A:THR41 3.4 111.0 1.0 C A:GLY44 3.5 115.6 1.0 C A:THR41 3.7 117.8 1.0 CZ A:PHE49 3.9 101.8 1.0 CA A:THR41 4.0 114.5 1.0 OD1 A:ASN50 4.0 104.5 1.0 CA A:GLY45 4.1 136.3 1.0 OD2 A:ASP47 4.2 99.0 1.0 N A:GLY45 4.2 136.1 1.0 N A:THR41 4.3 113.5 1.0 CB A:ASP39 4.3 112.9 1.0 N A:GLY44 4.4 114.3 1.0 ND2 A:ASN50 4.5 98.6 1.0 CE1 A:PHE49 4.6 100.5 1.0 CA A:GLY44 4.6 112.8 1.0 CG A:GLU55 4.6 102.0 1.0 CG2 A:THR41 4.7 101.3 1.0 CG A:ASN50 4.7 99.2 1.0 C A:GLY45 4.8 136.5 1.0 CE2 A:PHE49 4.9 99.2 1.0 O A:GLY45 4.9 134.9 1.0 N A:ILE42 5.0 128.6 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2472938267-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2472938267-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:120.8 occ:1.00 OE1 B:GLU113 2.9 87.6 1.0 OE2 B:GLU113 3.6 89.8 1.0 CD B:GLU113 3.7 87.7 1.0 OE1 B:GLU110 4.7 62.8 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2472938267-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2472938267-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:79.1 occ:1.00 O C:GLY44 2.3 84.1 1.0 O C:THR41 2.4 84.3 1.0 OE2 C:GLU55 2.4 74.1 1.0 OD2 C:ASP39 2.4 74.5 1.0 OG1 C:THR41 2.4 84.9 1.0 OE1 C:GLU55 2.5 78.3 1.0 OD1 C:ASP39 2.6 83.7 1.0 CD C:GLU55 2.8 74.8 1.0 CG C:ASP39 2.9 81.1 1.0 C C:THR41 3.4 85.8 1.0 CB C:THR41 3.4 86.4 1.0 C C:GLY44 3.6 83.9 1.0 CA C:THR41 3.8 86.9 1.0 N C:THR41 4.1 90.0 1.0 OD2 C:ASP47 4.2 84.7 1.0 CG C:GLU55 4.3 68.5 1.0 N C:GLY44 4.3 84.5 1.0 CA C:GLY45 4.4 85.0 1.0 CB C:ASP39 4.4 85.0 1.0 N C:GLY45 4.4 87.1 1.0 N C:ILE42 4.5 84.7 1.0 CA C:GLY44 4.6 84.4 1.0 CZ C:PHE49 4.6 70.7 1.0 NE2 C:HIS61 4.6 70.2 1.0 OD1 C:ASN50 4.6 76.4 1.0 CG2 C:THR41 4.8 78.2 1.0 ND2 C:ASN50 4.9 68.5 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2472938267-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2472938267-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:98.6 occ:1.00 O A:HOH616 2.9 88.2 1.0 O A:HOH604 3.3 80.1 1.0 OD2 E:ASP44 3.3 117.7 1.0 OG A:SER158 3.6 82.1 1.0 CB A:SER158 3.9 81.7 1.0 NZ A:LYS166 4.0 81.2 1.0 O A:GLY162 4.1 114.7 1.0 CG E:ASP44 4.4 119.2 1.0 CA A:SER158 4.6 78.8 1.0 O A:GLU196 4.7 96.0 1.0 OD1 E:ASP44 5.0 117.5 1.0 O A:HIS197 5.0 81.8 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