Calcium in PDB 6o5m: Tubulin-RB3_SLD-Ttl in Complex with Compound 10BB

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 10BB, PDB code: 6o5m 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)	49.76 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.966, 157.721, 181.615, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.3

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 10BB also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Tubulin-RB3_SLD-Ttl in Complex with Compound 10BB (pdb code 6o5m). 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 10BB, PDB code: 6o5m:
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 10BB


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 10BB within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:55.0 occ:1.00 O A:THR41 2.4 62.4 1.0 OD1 A:ASP39 2.4 51.9 1.0 OD2 A:ASP39 2.5 55.9 1.0 O A:GLY44 2.5 55.5 1.0 OE2 A:GLU55 2.5 49.2 1.0 O A:HOH620 2.5 45.9 1.0 OE1 A:GLU55 2.6 55.0 1.0 OG1 A:THR41 2.6 53.1 1.0 CG A:ASP39 2.8 52.9 1.0 CD A:GLU55 2.9 50.9 1.0 C A:GLY44 3.4 61.5 1.0 C A:THR41 3.5 64.0 1.0 CB A:THR41 3.5 56.1 1.0 CA A:THR41 3.9 62.8 1.0 N A:THR41 4.2 63.6 1.0 N A:GLY45 4.2 62.4 1.0 CA A:GLY45 4.2 60.5 1.0 N A:GLY44 4.3 68.0 1.0 CB A:ASP39 4.3 48.1 1.0 CG A:GLU55 4.4 47.8 1.0 CA A:GLY44 4.4 64.7 1.0 CZ A:PHE49 4.4 53.3 1.0 NE2 A:HIS61 4.5 59.4 1.0 OD1 A:ASN50 4.6 44.2 1.0 N A:ILE42 4.6 72.6 1.0 CE1 A:PHE49 4.7 51.6 1.0 ND2 A:ASN50 4.8 48.2 1.0 CG2 A:THR41 4.9 51.9 1.0

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


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 10BB within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:36.7 occ:1.00 OG1 C:THR41 2.4 46.7 1.0 OE2 C:GLU55 2.4 35.4 1.0 O C:THR41 2.4 45.1 1.0 O C:HOH613 2.4 33.5 1.0 O C:GLY44 2.4 40.9 1.0 OD2 C:ASP39 2.4 39.5 1.0 OE1 C:GLU55 2.5 37.6 1.0 OD1 C:ASP39 2.6 38.1 1.0 CD C:GLU55 2.8 32.4 1.0 CG C:ASP39 2.8 37.8 1.0 CB C:THR41 3.4 45.6 1.0 C C:THR41 3.4 40.3 1.0 C C:GLY44 3.5 43.4 1.0 CA C:THR41 3.8 43.0 1.0 CA C:GLY45 4.0 43.6 1.0 N C:THR41 4.1 47.0 1.0 N C:GLY45 4.1 41.1 1.0 O C:HOH601 4.2 38.7 1.0 CG C:GLU55 4.3 31.0 1.0 CB C:ASP39 4.3 39.4 1.0 N C:GLY44 4.4 44.4 1.0 OD2 C:ASP47 4.4 43.7 1.0 CA C:GLY44 4.5 44.5 1.0 NE2 C:HIS61 4.5 28.1 1.0 OD1 C:ASN50 4.6 29.1 1.0 N C:ILE42 4.7 37.3 1.0 CZ C:PHE49 4.7 33.0 1.0 CG2 C:THR41 4.7 36.8 1.0 ND2 C:ASN50 4.8 25.0 1.0 CE1 C:PHE49 4.9 32.6 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