Calcium in PDB 6o5n: Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB, PDB code: 6o5n 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)	41.78 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.301, 157.764, 182.084, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.5

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB 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 10AB (pdb code 6o5n). 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 10AB, PDB code: 6o5n:
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 10AB


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 10AB within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:85.5 occ:1.00 OG1 A:THR41 2.4 86.0 1.0 OE2 A:GLU55 2.4 83.1 1.0 OD1 A:ASP39 2.4 74.1 1.0 O A:GLY44 2.5 81.0 1.0 O A:THR41 2.6 81.8 1.0 OE1 A:GLU55 2.8 84.4 1.0 OD2 A:ASP39 2.8 74.0 1.0 CG A:ASP39 2.9 73.2 1.0 CD A:GLU55 2.9 82.6 1.0 CB A:THR41 3.5 85.8 1.0 C A:GLY44 3.5 81.7 1.0 C A:THR41 3.7 85.3 1.0 OD2 A:ASP47 3.8 78.1 1.0 CZ A:PHE49 3.8 68.8 1.0 OD1 A:ASN50 3.9 74.3 1.0 CA A:GLY45 4.0 85.3 1.0 CA A:THR41 4.1 85.0 1.0 N A:GLY45 4.2 83.3 1.0 CB A:ASP39 4.4 73.6 1.0 CG A:GLU55 4.4 80.1 1.0 N A:THR41 4.4 82.7 1.0 ND2 A:ASN50 4.5 71.0 1.0 NE2 A:HIS61 4.6 85.8 1.0 CE1 A:PHE49 4.6 66.7 1.0 N A:GLY44 4.6 82.7 1.0 CE2 A:PHE49 4.6 68.5 1.0 CA A:GLY44 4.7 82.2 1.0 CG A:ASN50 4.7 71.5 1.0 CG2 A:THR41 4.7 86.0 1.0 N A:ILE42 4.9 84.5 1.0 CG A:ASP47 5.0 78.6 1.0

Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB


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 10AB within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:56.2 occ:1.00 OE2 C:GLU55 2.3 52.0 1.0 OG1 C:THR41 2.3 63.3 1.0 OD1 C:ASP39 2.4 61.8 1.0 O C:GLY44 2.6 69.6 1.0 O C:THR41 2.6 66.7 1.0 OD2 C:ASP39 2.6 59.9 1.0 OE1 C:GLU55 2.7 53.1 1.0 CD C:GLU55 2.8 52.0 1.0 CG C:ASP39 2.9 60.9 1.0 CB C:THR41 3.5 64.1 1.0 C C:GLY44 3.6 70.6 1.0 C C:THR41 3.6 67.8 1.0 OD2 C:ASP47 4.0 63.6 1.0 CA C:THR41 4.0 66.2 1.0 CA C:GLY45 4.0 73.4 1.0 N C:GLY45 4.2 71.7 1.0 OD1 C:ASN50 4.2 49.2 1.0 N C:THR41 4.2 65.8 1.0 CZ C:PHE49 4.3 47.4 1.0 CG C:GLU55 4.3 49.8 1.0 CB C:ASP39 4.4 62.3 1.0 ND2 C:ASN50 4.6 48.3 1.0 NE2 C:HIS61 4.6 47.5 1.0 CE1 C:PHE49 4.6 47.3 1.0 N C:GLY44 4.6 72.1 1.0 CA C:GLY44 4.7 70.1 1.0 CG2 C:THR41 4.7 63.5 1.0 N C:ILE42 4.8 70.2 1.0 CG C:ASN50 4.8 46.0 1.0

Q.Wang, K.E.Arnst, Y.Wang, G.Kumar, D.Ma, S.W.White, D.D.Miller, W.Li, W.Li. Structure-Guided Design, Synthesis, and Biological Evaluation of (2-(1H-Indol-3-Yl)-1H-Imidazol-4-Yl)(3,4,5-Trimethoxyphenyl) Methanone (Abi-231) Analogues Targeting the Colchicine Binding Site in Tubulin. J.Med.Chem. V. 62 6734 2019.
ISSN: ISSN 0022-2623
PubMed: 31251599
DOI: 10.1021/ACS.JMEDCHEM.9B00706