Calcium in PDB 6x1e: Tubulin-RB3_SLD-Ttl in Complex with Compound 5L

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5L, PDB code: 6x1e 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)	49.91 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.36, 157.742, 182.163, 90, 90, 90
R / Rfree (%)	17 / 22.4

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

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

The binding sites of Calcium atom in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5L (pdb code 6x1e). 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 5L, PDB code: 6x1e:
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 5L


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 5L within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:72.3 occ:1.00 OD2 A:ASP39 2.4 64.1 1.0 O A:GLY44 2.4 78.9 1.0 OG1 A:THR41 2.4 100.0 1.0 O A:THR41 2.5 79.5 1.0 OD1 A:ASP39 2.5 53.0 1.0 OE2 A:GLU55 2.5 93.1 1.0 OE1 A:GLU55 2.5 84.0 1.0 CG A:ASP39 2.7 60.5 1.0 CD A:GLU55 2.8 82.1 1.0 CB A:THR41 3.5 82.0 1.0 C A:THR41 3.5 75.7 1.0 C A:GLY44 3.6 75.8 1.0 CA A:THR41 3.9 81.6 1.0 CZ A:PHE49 4.2 68.8 1.0 N A:THR41 4.2 81.8 1.0 CB A:ASP39 4.3 68.0 1.0 CG A:GLU55 4.3 64.0 1.0 CA A:GLY45 4.3 75.0 1.0 N A:GLY45 4.4 65.3 1.0 N A:GLY44 4.5 79.5 1.0 OD1 A:ASN50 4.6 60.5 1.0 OD2 A:ASP47 4.6 69.8 1.0 CA A:GLY44 4.7 79.9 1.0 NE2 A:HIS61 4.7 64.5 1.0 N A:ILE42 4.7 75.3 1.0 ND2 A:ASN50 4.8 47.0 1.0 CG2 A:THR41 4.8 70.9 1.0 CE1 A:PHE49 4.9 59.7 1.0

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


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 5L within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:51.1 occ:1.00 OG1 C:THR41 2.3 63.1 1.0 OE2 C:GLU55 2.3 58.2 1.0 O C:THR41 2.3 71.6 1.0 O C:HOH605 2.3 53.6 1.0 OD2 C:ASP39 2.4 53.6 1.0 OE1 C:GLU55 2.4 49.0 1.0 OD1 C:ASP39 2.5 52.3 1.0 O C:GLY44 2.5 59.1 1.0 CD C:GLU55 2.7 44.2 1.0 CG C:ASP39 2.8 46.2 1.0 C C:THR41 3.4 55.2 1.0 CB C:THR41 3.5 60.4 1.0 C C:GLY44 3.6 55.9 1.0 CA C:THR41 3.9 46.0 1.0 CG C:GLU55 4.2 39.8 1.0 N C:THR41 4.2 45.2 1.0 CA C:GLY45 4.2 40.7 1.0 CB C:ASP39 4.3 59.2 1.0 N C:GLY45 4.3 54.0 1.0 OD2 C:ASP47 4.4 57.0 1.0 N C:ILE42 4.5 49.8 1.0 OD1 C:ASN50 4.5 45.7 1.0 CA C:GLY44 4.6 57.7 1.0 NE2 C:HIS61 4.6 31.5 1.0 CZ C:PHE49 4.6 29.5 1.0 N C:GLY44 4.6 54.8 1.0 CG2 C:THR41 4.7 48.0 1.0 CE1 C:PHE49 4.9 31.3 1.0 ND2 C:ASN50 4.9 32.7 1.0 CA C:ILE42 5.0 55.6 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