Calcium in PDB 7daf: Ixa in Complex with Tubulin

The structure of Ixa in Complex with Tubulin, PDB code: 7daf was solved by C.Wu, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.50 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.162, 158.179, 181.875, 90, 90, 90
R / Rfree (%)	17.4 / 22.2

The structure of Ixa in Complex with Tubulin also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Ixa in Complex with Tubulin (pdb code 7daf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ixa in Complex with Tubulin, PDB code: 7daf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Ixa in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ixa in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:54.5 occ:1.00 O A:GLY44 2.2 56.6 1.0 OD1 A:ASP39 2.5 46.0 1.0 OG1 A:THR41 2.5 64.2 1.0 OE2 A:GLU55 2.5 56.0 1.0 OD2 A:ASP39 2.6 52.9 1.0 O A:THR41 2.7 64.0 1.0 OE1 A:GLU55 2.9 53.3 1.0 CG A:ASP39 2.9 57.1 1.0 CD A:GLU55 3.1 54.0 1.0 C A:GLY44 3.4 60.4 1.0 CB A:THR41 3.6 56.1 1.0 C A:THR41 3.6 59.9 1.0 CA A:GLY45 3.9 66.2 1.0 OD2 A:ASP47 3.9 72.2 1.0 CA A:THR41 4.0 65.8 1.0 N A:GLY45 4.1 49.5 1.0 N A:THR41 4.2 57.6 1.0 CZ A:PHE49 4.2 47.4 1.0 N A:GLY44 4.4 58.8 1.0 CB A:ASP39 4.4 50.8 1.0 O A:HOH604 4.4 48.8 1.0 CA A:GLY44 4.5 57.3 1.0 CG A:GLU55 4.6 50.6 1.0 OD1 A:ASN50 4.6 49.5 1.0 ND2 A:ASN50 4.8 45.8 1.0 N A:ILE42 4.9 61.6 1.0 CG2 A:THR41 4.9 44.0 1.0 CE1 A:PHE49 4.9 52.8 1.0 C A:GLY45 5.0 64.3 1.0

Calcium binding site 2 out of 4 in the Ixa in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ixa in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:82.1 occ:1.00 OE2 B:GLU111 2.6 78.6 1.0 CD B:GLU111 3.5 66.5 1.0 OE1 B:GLU111 3.7 77.2 1.0 OE1 B:GLU108 4.4 38.4 1.0 CG B:GLU111 5.0 46.8 1.0

Calcium binding site 3 out of 4 in the Ixa in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ixa in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:41.6 occ:1.00 OD2 C:ASP39 2.4 48.6 1.0 O C:THR41 2.4 48.8 1.0 OG1 C:THR41 2.4 55.1 1.0 O C:GLY44 2.5 48.7 1.0 OE2 C:GLU55 2.5 49.6 1.0 OE1 C:GLU55 2.5 38.6 1.0 OD1 C:ASP39 2.5 43.0 1.0 CG C:ASP39 2.8 41.9 1.0 CD C:GLU55 2.9 38.8 1.0 C C:THR41 3.4 41.4 1.0 CB C:THR41 3.4 54.2 1.0 C C:GLY44 3.5 47.6 1.0 CA C:THR41 3.8 43.6 1.0 CA C:GLY45 4.1 49.2 1.0 N C:THR41 4.1 47.0 1.0 N C:GLY45 4.1 52.2 1.0 OD2 C:ASP47 4.1 59.0 1.0 CB C:ASP39 4.3 40.9 1.0 CG C:GLU55 4.4 31.4 1.0 O C:HOH619 4.5 34.1 1.0 N C:GLY44 4.5 44.5 1.0 CA C:GLY44 4.5 50.1 1.0 OD1 C:ASN50 4.6 32.1 1.0 N C:ILE42 4.6 38.1 1.0 CZ C:PHE49 4.6 31.5 1.0 NE2 C:HIS61 4.7 37.7 1.0 CG2 C:THR41 4.8 31.7 1.0 CE1 C:PHE49 4.9 35.9 1.0 ND2 C:ASN50 5.0 25.2 1.0

Calcium binding site 4 out of 4 in the Ixa in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ixa in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:71.8 occ:1.00 OD2 E:ASP44 2.6 75.5 1.0 O A:HOH706 2.7 61.4 1.0 O A:GLU196 2.9 41.7 1.0 O A:HOH692 3.0 55.2 1.0 CG E:ASP44 3.3 71.9 1.0 OD1 E:ASP44 3.3 69.3 1.0 C A:GLU196 4.1 39.9 1.0 O A:HOH751 4.5 43.8 1.0 CA A:HIS197 4.6 27.7 1.0 OG A:SER158 4.6 42.4 1.0 N A:HIS197 4.8 27.0 1.0 CB E:ASP44 4.8 80.1 1.0

Q.Xiao, T.Xue, W.Shuai, C.Wu, Z.Zhang, T.Zhang, S.Zeng, B.Sun, Y.Wang. High-Resolution X-Ray Structure of Three Microtubule-Stabilizing Agents in Complex with Tubulin Provide A Rationale For Drug Design. Biochem.Biophys.Res.Commun. V. 534 330 2021.
ISSN: ESSN 1090-2104
PubMed: 33272565
DOI: 10.1016/J.BBRC.2020.11.082