Calcium in PDB 6bry: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A, PDB code: 6bry was solved by G.Kumar, Y.Wang, W.Li, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.089, 157.766, 181.456, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.6

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A (pdb code 6bry). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A, PDB code: 6bry:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:59.7 occ:1.00 OD2 A:ASP39 2.4 51.2 1.0 OE1 A:GLU55 2.4 53.6 1.0 O A:THR41 2.4 60.9 1.0 O A:GLY44 2.5 55.5 1.0 OE2 A:GLU55 2.6 59.9 1.0 OD1 A:ASP39 2.7 54.5 1.0 OG1 A:THR41 2.7 70.5 1.0 CD A:GLU55 2.8 56.3 1.0 CG A:ASP39 2.8 56.2 1.0 C A:GLY44 3.4 60.7 1.0 C A:THR41 3.4 61.8 1.0 CB A:THR41 3.4 68.3 1.0 CA A:THR41 3.9 64.9 1.0 N A:GLY45 4.2 63.6 1.0 N A:GLY44 4.2 63.9 1.0 N A:THR41 4.3 64.5 1.0 CA A:GLY45 4.3 65.8 1.0 CA A:GLY44 4.3 63.6 1.0 CG A:GLU55 4.3 55.6 1.0 CB A:ASP39 4.4 61.5 1.0 OD1 A:ASN50 4.4 52.3 1.0 OD2 A:ASP47 4.5 56.0 1.0 CZ A:PHE49 4.5 50.8 1.0 N A:ILE42 4.6 63.2 1.0 CE1 A:PHE49 4.7 51.2 1.0 NE2 A:HIS61 4.7 58.2 1.0 ND2 A:ASN50 4.8 44.1 1.0 CG2 A:THR41 4.9 69.0 1.0

Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:36.8 occ:1.00 O C:THR41 2.4 44.3 1.0 O C:HOH614 2.4 31.8 1.0 OE1 C:GLU55 2.5 31.7 1.0 OE2 C:GLU55 2.5 27.9 1.0 OD1 C:ASP39 2.5 42.2 1.0 OG1 C:THR41 2.6 51.8 1.0 O C:GLY44 2.6 44.7 1.0 OD2 C:ASP39 2.7 39.9 1.0 CD C:GLU55 2.8 36.8 1.0 CG C:ASP39 3.0 43.0 1.0 C C:THR41 3.4 44.0 1.0 CB C:THR41 3.4 46.9 1.0 C C:GLY44 3.5 44.5 1.0 CA C:THR41 3.8 42.5 1.0 N C:THR41 4.1 43.9 1.0 N C:GLY45 4.2 45.7 1.0 CA C:GLY45 4.2 45.2 1.0 O C:HOH607 4.3 32.5 1.0 CG C:GLU55 4.3 34.8 1.0 N C:GLY44 4.3 43.2 1.0 CA C:GLY44 4.4 43.5 1.0 OD2 C:ASP47 4.5 39.9 1.0 CB C:ASP39 4.5 46.9 1.0 OD1 C:ASN50 4.5 30.4 1.0 N C:ILE42 4.6 45.4 1.0 NE2 C:HIS61 4.8 27.6 1.0 CG2 C:THR41 4.8 45.9 1.0 CZ C:PHE49 4.8 29.2 1.0 CE1 C:PHE49 5.0 31.5 1.0

S.Banerjee, K.E.Arnst, Y.Wang, G.Kumar, S.Deng, L.Yang, G.B.Li, J.Yang, S.W.White, W.Li, D.D.Miller. Heterocyclic-Fused Pyrimidines As Novel Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site: Structural Basis and Antitumor Efficacy. J. Med. Chem. V. 61 1704 2018.
ISSN: ISSN 1520-4804
PubMed: 29406710
DOI: 10.1021/ACS.JMEDCHEM.7B01858