Calcium in PDB 6jcj: Structure of Crolibulin in Complex with Tubulin

The structure of Structure of Crolibulin in Complex with Tubulin, PDB code: 6jcj was solved by Z.Zhang, J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.42 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.544, 157.329, 184.031, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 28.2

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

Magnesium	(Mg)	3 atoms
Bromine	(Br)	2 atoms

The binding sites of Calcium atom in the Structure of Crolibulin in Complex with Tubulin (pdb code 6jcj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Crolibulin in Complex with Tubulin, PDB code: 6jcj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Crolibulin 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 Structure of Crolibulin in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:54.4 occ:1.00 OE2 A:GLU55 2.3 64.1 1.0 OD2 A:ASP39 2.4 58.4 1.0 O A:GLY44 2.5 55.1 1.0 OG1 A:THR41 2.5 66.3 1.0 O A:THR41 2.5 59.3 1.0 OD1 A:ASP39 2.6 53.5 1.0 CG A:ASP39 2.8 54.9 1.0 OE1 A:GLU55 3.0 62.7 1.0 CD A:GLU55 3.0 64.2 1.0 CB A:THR41 3.6 65.3 1.0 C A:THR41 3.6 63.1 1.0 C A:GLY44 3.6 60.2 1.0 CA A:THR41 4.0 63.0 1.0 CA A:GLY45 4.1 63.9 1.0 N A:GLY45 4.2 61.3 1.0 CZ A:PHE49 4.2 56.1 1.0 OD2 A:ASP47 4.3 49.5 1.0 N A:THR41 4.3 59.4 1.0 CB A:ASP39 4.3 54.2 1.0 OD1 A:ASN50 4.4 52.3 1.0 NE2 A:HIS61 4.4 47.3 1.0 ND2 A:ASN50 4.5 47.9 1.0 CG A:GLU55 4.5 63.8 1.0 CA A:GLY44 4.7 58.6 1.0 N A:GLY44 4.7 55.9 1.0 N A:ILE42 4.7 60.3 1.0 CG2 A:THR41 4.8 66.5 1.0 CG A:ASN50 4.9 47.0 1.0 CE1 A:PHE49 4.9 56.4 1.0

Calcium binding site 2 out of 2 in the Structure of Crolibulin 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 Structure of Crolibulin in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:37.9 occ:1.00 OG1 C:THR41 1.9 64.1 1.0 O C:THR41 2.3 57.4 1.0 OE1 C:GLU55 2.3 35.6 1.0 OD2 C:ASP39 2.4 33.4 1.0 OE2 C:GLU55 2.5 35.6 1.0 OD1 C:ASP39 2.5 34.9 1.0 O C:GLY44 2.5 46.2 1.0 CD C:GLU55 2.7 33.0 1.0 CG C:ASP39 2.8 36.4 1.0 C C:THR41 3.2 53.8 1.0 CB C:THR41 3.2 60.1 1.0 CA C:THR41 3.6 53.8 1.0 C C:GLY44 3.6 46.2 1.0 OD2 C:ASP47 4.0 40.8 1.0 CG2 C:THR41 4.1 63.7 1.0 N C:THR41 4.1 49.1 1.0 CG C:GLU55 4.2 31.5 1.0 CB C:ASP39 4.3 39.2 1.0 N C:ILE42 4.3 53.0 1.0 NE2 C:HIS61 4.4 28.9 1.0 N C:GLY45 4.4 45.8 1.0 N C:GLY44 4.5 45.4 1.0 CA C:GLY45 4.5 48.0 1.0 CA C:GLY44 4.6 46.4 1.0 OD1 C:ASN50 4.6 23.0 1.0 ND2 C:ASN50 4.9 21.5 1.0 CA C:ILE42 4.9 47.1 1.0 CZ C:PHE49 4.9 28.9 1.0 CE1 C:PHE49 4.9 28.9 1.0

Z.Zhang, C.Wang, L.Ma, X.Jiang, C.Wu, Y.Wang, Y.Jiang, W.Zheng, Y.Yang, Y.Ma, J.Yang. Molecular Mechanism of Crolibulin in Complex with Tubulin Provides A Rationale For Drug Design. Biochem. Biophys. Res. V. 511 381 2019COMMUN..
ISSN: ESSN 1090-2104
PubMed: 30803758
DOI: 10.1016/J.BBRC.2019.02.064