Calcium in PDB 6d88: Tubulin-RB3_SLD-Ttl in Complex with Compound 13F

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 13F, PDB code: 6d88 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)	45.65 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.536, 157.894, 182.025, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.6

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 13F also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Tubulin-RB3_SLD-Ttl in Complex with Compound 13F (pdb code 6d88). 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 13F, PDB code: 6d88:
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 13F


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 13F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:63.5 occ:1.00 OE2 A:GLU55 2.3 64.9 1.0 O A:GLY44 2.4 72.9 1.0 O A:THR41 2.8 78.8 1.0 OD2 A:ASP39 2.8 62.4 1.0 OD1 A:ASP39 2.9 60.0 1.0 CD A:GLU55 3.1 64.2 1.0 OE1 A:GLU55 3.1 67.3 1.0 CB A:THR41 3.1 74.2 1.0 CG A:ASP39 3.2 62.1 1.0 OG1 A:THR41 3.3 75.4 1.0 C A:GLY44 3.4 80.0 1.0 C A:THR41 3.7 76.9 1.0 CA A:GLY45 3.7 84.8 1.0 CA A:THR41 3.9 75.8 1.0 N A:GLY45 3.9 83.9 1.0 OD2 A:ASP47 4.0 65.2 1.0 OD1 A:ASN50 4.1 66.1 1.0 N A:THR41 4.2 71.1 1.0 CG2 A:THR41 4.3 70.9 1.0 CZ A:PHE49 4.5 61.8 1.0 CG A:GLU55 4.5 63.5 1.0 CA A:GLY44 4.5 79.8 1.0 N A:GLY44 4.7 77.2 1.0 CB A:ASP39 4.7 61.4 1.0 C A:GLY45 4.7 82.3 1.0 N A:ILE42 4.9 73.7 1.0 CG A:ASP47 4.9 61.7 1.0 ND2 A:ASN50 4.9 60.3 1.0 CG A:ASN50 5.0 63.0 1.0

Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 13F


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 13F within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:54.2 occ:1.00 OE2 C:GLU55 2.2 59.8 1.0 OG1 C:THR41 2.2 60.6 1.0 OD2 C:ASP39 2.4 45.9 1.0 OD1 C:ASP39 2.4 44.6 1.0 O C:THR41 2.5 46.0 1.0 O C:GLY44 2.6 61.2 1.0 CG C:ASP39 2.7 47.1 1.0 OE1 C:GLU55 2.8 57.5 1.0 CD C:GLU55 2.8 54.4 1.0 CB C:THR41 3.5 53.8 1.0 C C:THR41 3.5 49.7 1.0 C C:GLY44 3.6 60.4 1.0 CA C:THR41 3.9 53.4 1.0 CA C:GLY45 4.0 52.2 1.0 N C:THR41 4.1 54.8 1.0 OD2 C:ASP47 4.2 53.5 1.0 N C:GLY45 4.2 55.8 1.0 CB C:ASP39 4.2 52.8 1.0 OD1 C:ASN50 4.3 46.5 1.0 CG C:GLU55 4.3 45.6 1.0 CZ C:PHE49 4.4 35.4 1.0 CA C:GLY44 4.6 61.4 1.0 CG2 C:THR41 4.6 52.8 1.0 N C:GLY44 4.6 62.4 1.0 CE1 C:PHE49 4.7 38.2 1.0 N C:ILE42 4.7 50.0 1.0 NE2 C:HIS61 4.8 35.3 1.0 ND2 C:ASN50 4.9 46.0 1.0

Q.Wang, K.E.Arnst, Y.Wang, G.Kumar, D.Ma, H.Chen, Z.Wu, J.Yang, S.W.White, D.D.Miller, W.Li. Structural Modification of the 3,4,5-Trimethoxyphenyl Moiety in the Tubulin Inhibitor Veru-111 Leads to Improved Antiproliferative Activities. J. Med. Chem. V. 61 7877 2018.
ISSN: ISSN 1520-4804
PubMed: 30122035
DOI: 10.1021/ACS.JMEDCHEM.8B00827