Calcium in PDB 6br1: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4A

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4A, PDB code: 6br1 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)	49.64 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.927, 157.613, 180.989, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.5

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4A 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 4A (pdb code 6br1). 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 4A, PDB code: 6br1:
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 4A


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:59.7 occ:1.00 O A:THR41 2.4 68.7 1.0 OD2 A:ASP39 2.4 53.6 1.0 OD1 A:ASP39 2.4 55.3 1.0 O A:GLY44 2.4 59.4 1.0 OG1 A:THR41 2.5 55.7 1.0 OE2 A:GLU55 2.6 58.5 1.0 OE1 A:GLU55 2.7 55.1 1.0 CG A:ASP39 2.7 53.4 1.0 CD A:GLU55 3.0 56.0 1.0 C A:THR41 3.4 68.9 1.0 CB A:THR41 3.5 60.1 1.0 C A:GLY44 3.5 61.6 1.0 CA A:THR41 3.9 66.5 1.0 N A:THR41 4.1 68.4 1.0 CB A:ASP39 4.2 50.1 1.0 CA A:GLY45 4.3 60.0 1.0 N A:GLY45 4.3 62.7 1.0 OD2 A:ASP47 4.3 58.8 1.0 N A:GLY44 4.4 63.1 1.0 CZ A:PHE49 4.4 48.5 1.0 CG A:GLU55 4.5 52.4 1.0 CA A:GLY44 4.5 63.0 1.0 OD1 A:ASN50 4.6 57.3 1.0 N A:ILE42 4.6 68.8 1.0 NE2 A:HIS61 4.6 60.3 1.0 CG2 A:THR41 4.8 54.3 1.0 ND2 A:ASN50 4.8 49.5 1.0 CE1 A:PHE49 4.9 49.1 1.0

Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4A


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:34.9 occ:1.00 O C:THR41 2.4 46.1 1.0 O C:HOH611 2.4 29.9 1.0 OE1 C:GLU55 2.4 28.4 1.0 OE2 C:GLU55 2.4 28.1 1.0 O C:GLY44 2.4 41.8 1.0 OG1 C:THR41 2.5 40.6 1.0 OD2 C:ASP39 2.5 38.0 1.0 OD1 C:ASP39 2.5 36.1 1.0 CD C:GLU55 2.7 31.3 1.0 CG C:ASP39 2.9 39.0 1.0 C C:THR41 3.4 41.1 1.0 CB C:THR41 3.5 39.7 1.0 C C:GLY44 3.5 41.4 1.0 CA C:THR41 3.8 39.5 1.0 N C:THR41 4.1 43.5 1.0 O C:HOH603 4.1 40.4 1.0 CA C:GLY45 4.2 42.5 1.0 O C:HOH605 4.2 30.0 1.0 CG C:GLU55 4.2 31.2 1.0 N C:GLY45 4.2 41.3 1.0 CB C:ASP39 4.4 42.5 1.0 N C:GLY44 4.4 44.6 1.0 OD2 C:ASP47 4.4 43.1 1.0 CA C:GLY44 4.5 43.5 1.0 OD1 C:ASN50 4.6 30.6 1.0 N C:ILE42 4.6 38.6 1.0 NE2 C:HIS61 4.6 27.9 1.0 CZ C:PHE49 4.7 33.3 1.0 CG2 C:THR41 4.8 35.6 1.0 ND2 C:ASN50 4.9 27.9 1.0 O C:HOH707 5.0 37.4 1.0 CE1 C:PHE49 5.0 32.5 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