Calcium in PDB 6x1c: Tubulin-RB3_SLD-Ttl in Complex with Compound 5J

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5J, PDB code: 6x1c was solved by S.W.White, M.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.14 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.345, 158.32, 181.949, 90, 90, 90
R / Rfree (%)	17.4 / 21.6

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5J also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5J (pdb code 6x1c). 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 Compound 5J, PDB code: 6x1c:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5J


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 Compound 5J within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:65.5 occ:1.00 OD2 A:ASP39 2.3 71.9 1.0 OE2 A:GLU55 2.4 85.2 1.0 O A:THR41 2.4 95.3 1.0 OG1 A:THR41 2.4 100.0 1.0 OD1 A:ASP39 2.4 50.1 1.0 OE1 A:GLU55 2.4 68.4 1.0 O A:GLY44 2.4 67.0 1.0 CG A:ASP39 2.7 55.0 1.0 CD A:GLU55 2.7 71.1 1.0 CB A:THR41 3.4 89.2 1.0 C A:THR41 3.4 87.2 1.0 C A:GLY44 3.6 74.9 1.0 CA A:THR41 3.8 88.9 1.0 N A:THR41 4.1 84.2 1.0 CB A:ASP39 4.2 61.2 1.0 CG A:GLU55 4.2 67.2 1.0 CA A:GLY45 4.3 75.1 1.0 CZ A:PHE49 4.3 55.9 1.0 OD2 A:ASP47 4.3 67.8 1.0 N A:GLY45 4.4 74.9 1.0 OD1 A:ASN50 4.5 47.5 1.0 N A:GLY44 4.5 74.0 1.0 N A:ILE42 4.6 80.7 1.0 CA A:GLY44 4.7 75.8 1.0 NE2 A:HIS61 4.7 51.5 1.0 ND2 A:ASN50 4.7 44.1 1.0 CG2 A:THR41 4.7 75.3 1.0 CE1 A:PHE49 4.9 50.7 1.0

Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5J


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 Compound 5J within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:43.0 occ:1.00 OD2 C:ASP39 2.3 60.4 1.0 O C:THR41 2.4 53.5 1.0 OE2 C:GLU55 2.4 44.1 1.0 OD1 C:ASP39 2.4 56.8 1.0 OG1 C:THR41 2.4 57.2 1.0 OE1 C:GLU55 2.4 44.3 1.0 O C:HOH602 2.5 41.5 1.0 O C:GLY44 2.5 53.3 1.0 CG C:ASP39 2.7 55.3 1.0 CD C:GLU55 2.7 44.1 1.0 C C:THR41 3.4 45.5 1.0 CB C:THR41 3.5 50.1 1.0 C C:GLY44 3.5 57.5 1.0 CA C:THR41 3.9 41.6 1.0 N C:THR41 4.1 44.0 1.0 CA C:GLY45 4.1 54.6 1.0 CB C:ASP39 4.2 65.5 1.0 N C:GLY45 4.2 56.1 1.0 CG C:GLU55 4.2 30.7 1.0 OD2 C:ASP47 4.4 55.1 1.0 NE2 C:HIS61 4.5 31.2 1.0 CA C:GLY44 4.5 59.9 1.0 N C:GLY44 4.6 62.4 1.0 OD1 C:ASN50 4.6 38.9 1.0 N C:ILE42 4.6 45.5 1.0 CZ C:PHE49 4.6 29.9 1.0 CG2 C:THR41 4.8 38.4 1.0 ND2 C:ASN50 4.9 33.6 1.0 CE1 C:PHE49 4.9 36.8 1.0

S.Banerjee, F.Mahmud, S.Deng, L.Ma, M.K.Yun, S.O.Fakayode, K.E.Arnst, L.Yang, H.Chen, Z.Wu, P.B.Lukka, K.Parmar, B.Meibohm, S.W.White, Y.Wang, W.Li, D.D.Miller. X-Ray Crystallography-Guided Design, Antitumor Efficacy, and Qsar Analysis of Metabolically Stable Cyclopenta-Pyrimidinyl Dihydroquinoxalinone As A Potent Tubulin Polymerization Inhibitor. J.Med.Chem. V. 64 13072 2021.
ISSN: ISSN 0022-2623
PubMed: 34406768
DOI: 10.1021/ACS.JMEDCHEM.1C01202