Calcium in PDB 7z2n: Tubulin-18-Complex

The structure of Tubulin-18-Complex, PDB code: 7z2n was solved by T.Muehlethaler, A.E.Prota, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.82 / 2.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.016, 157.703, 180.154, 90, 90, 90
R / Rfree (%)	18.9 / 22.4

The structure of Tubulin-18-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-18-Complex (pdb code 7z2n). 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-18-Complex, PDB code: 7z2n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:71.7 occ:1.00 OD1 A:ASP39 2.4 77.1 1.0 O A:HOH626 2.4 72.8 1.0 O A:THR41 2.4 84.4 1.0 O A:GLY44 2.4 77.5 1.0 OE2 A:GLU55 2.5 70.5 1.0 OD2 A:ASP39 2.5 76.0 1.0 OG1 A:THR41 2.6 72.0 1.0 OE1 A:GLU55 2.7 75.7 1.0 CG A:ASP39 2.8 77.4 1.0 CD A:GLU55 2.9 74.7 1.0 C A:THR41 3.5 84.4 1.0 CB A:THR41 3.5 77.8 1.0 C A:GLY44 3.6 80.6 1.0 CA A:THR41 3.9 84.0 1.0 N A:THR41 4.1 84.5 1.0 O A:HOH613 4.2 73.9 1.0 CB A:ASP39 4.3 74.2 1.0 CA A:GLY45 4.4 78.6 1.0 CZ A:PHE49 4.4 66.0 1.0 CG A:GLU55 4.4 70.6 1.0 OD1 A:ASN50 4.4 68.7 1.0 N A:GLY45 4.5 79.1 1.0 OD2 A:ASP47 4.5 70.2 1.0 N A:GLY44 4.5 81.4 1.0 N A:ILE42 4.6 90.3 1.0 CA A:GLY44 4.7 81.5 1.0 NE2 A:HIS61 4.7 69.6 1.0 CE1 A:PHE49 4.8 64.2 1.0 ND2 A:ASN50 4.8 66.3 1.0 CG2 A:THR41 4.9 70.5 1.0

Calcium binding site 2 out of 4 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:93.9 occ:1.00 O B:HOH644 2.4 68.1 1.0 OE1 B:GLU113 2.8 77.6 1.0 OE2 B:GLU113 3.5 81.1 1.0 CD B:GLU113 3.5 74.2 1.0 CG B:GLU113 5.0 64.3 1.0

Calcium binding site 3 out of 4 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:61.2 occ:1.00 O C:GLY44 2.4 63.5 1.0 O C:THR41 2.4 64.0 1.0 O C:HOH604 2.5 50.6 1.0 OE1 C:GLU55 2.5 55.2 1.0 OD2 C:ASP39 2.5 56.2 1.0 OD1 C:ASP39 2.5 57.4 1.0 OG1 C:THR41 2.5 61.6 1.0 OE2 C:GLU55 2.6 57.9 1.0 CG C:ASP39 2.9 55.5 1.0 CD C:GLU55 2.9 58.9 1.0 C C:THR41 3.4 68.2 1.0 C C:GLY44 3.5 65.5 1.0 CB C:THR41 3.5 63.7 1.0 CA C:THR41 3.9 65.2 1.0 O C:HOH608 4.1 57.5 1.0 CA C:GLY45 4.1 61.5 1.0 N C:THR41 4.2 62.3 1.0 N C:GLY45 4.2 64.3 1.0 OD2 C:ASP47 4.3 66.6 1.0 CB C:ASP39 4.4 59.2 1.0 CG C:GLU55 4.4 54.6 1.0 N C:GLY44 4.5 67.7 1.0 CA C:GLY44 4.5 65.2 1.0 N C:ILE42 4.6 64.0 1.0 OD1 C:ASN50 4.6 52.9 1.0 NE2 C:HIS61 4.7 48.6 1.0 CZ C:PHE49 4.7 49.0 1.0 CG2 C:THR41 4.9 50.4 1.0 ND2 C:ASN50 4.9 49.6 1.0 CE1 C:PHE49 5.0 48.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:95.8 occ:1.00 O A:HOH706 3.1 58.7 1.0 OD2 E:ASP44 3.4 108.5 1.0 OG A:SER158 4.0 61.5 1.0 O A:GLU196 4.4 57.7 1.0 O A:GLY162 4.4 70.2 1.0 CG E:ASP44 4.5 104.8 1.0 NZ A:LYS166 4.6 56.7 1.0 CB A:SER158 4.6 57.2 1.0 OD1 A:ASP199 4.9 55.9 1.0 OD1 E:ASP44 4.9 98.3 1.0 O A:HIS197 4.9 59.9 1.0 CA A:HIS197 5.0 51.5 1.0

N.M.De La Roche, T.Muhlethaler, R.M.C.Di Martino, J.A.Ortega, D.Gioia, B.Roy, A.E.Prota, M.O.Steinmetz, A.Cavalli. Novel Fragment-Derived Colchicine-Site Binders As Microtubule-Destabilizing Agents. Eur.J.Med.Chem. V. 241 14614 2022.
ISSN: ISSN 0223-5234
PubMed: 35939994
DOI: 10.1016/J.EJMECH.2022.114614