Calcium in PDB 6o61: Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-231

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-231, PDB code: 6o61 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)	48.16 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.257, 157.092, 184.039, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.4

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-231 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 Abi-231 (pdb code 6o61). 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 Abi-231, PDB code: 6o61:
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 Abi-231


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 Abi-231 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:71.7 occ:1.00 O A:GLY44 2.4 74.5 1.0 OE1 A:GLU55 2.4 81.1 1.0 OD1 A:ASP39 2.4 69.5 1.0 OD2 A:ASP39 2.5 66.4 1.0 O A:THR41 2.7 84.8 1.0 CG A:ASP39 2.8 68.5 1.0 CD A:GLU55 3.0 78.7 1.0 OE2 A:GLU55 3.1 80.2 1.0 CB A:THR41 3.1 91.5 1.0 C A:GLY44 3.3 69.0 1.0 C A:THR41 3.6 83.7 1.0 OG1 A:THR41 3.8 99.7 1.0 CA A:THR41 3.8 86.1 1.0 CA A:GLY45 3.9 74.4 1.0 N A:GLY45 4.0 68.5 1.0 CG2 A:THR41 4.0 93.9 1.0 OD1 A:ASN50 4.1 67.8 1.0 N A:THR41 4.2 79.5 1.0 CZ A:PHE49 4.3 58.2 1.0 CB A:ASP39 4.3 66.7 1.0 CA A:GLY44 4.4 70.6 1.0 OD1 A:ASP47 4.4 69.8 1.0 N A:GLY44 4.5 75.2 1.0 CG A:GLU55 4.5 71.4 1.0 ND2 A:ASN50 4.7 63.1 1.0 N A:ILE42 4.8 80.8 1.0 CE1 A:PHE49 4.8 54.3 1.0 CG A:ASN50 4.9 63.8 1.0 O A:HOH650 4.9 48.2 1.0 C A:GLY45 4.9 74.9 1.0 NE2 A:HIS61 5.0 69.0 1.0

Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-231


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 Abi-231 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:55.3 occ:1.00 OG1 C:THR41 2.2 67.8 1.0 OE2 C:GLU55 2.3 49.7 1.0 OD2 C:ASP39 2.3 56.7 1.0 O C:THR41 2.5 64.5 1.0 O C:GLY44 2.5 61.8 1.0 OD1 C:ASP39 2.5 50.3 1.0 OE1 C:GLU55 2.6 50.9 1.0 CG C:ASP39 2.7 53.7 1.0 CD C:GLU55 2.8 45.3 1.0 C C:THR41 3.5 58.0 1.0 CB C:THR41 3.5 62.4 1.0 C C:GLY44 3.5 54.8 1.0 CA C:THR41 3.9 56.6 1.0 OD1 C:ASP47 4.2 59.8 1.0 N C:THR41 4.2 56.5 1.0 CB C:ASP39 4.2 57.8 1.0 CG C:GLU55 4.2 34.5 1.0 CA C:GLY45 4.3 48.2 1.0 N C:GLY45 4.3 46.7 1.0 CG2 C:THR41 4.3 57.9 1.0 OD1 C:ASN50 4.4 43.6 1.0 NE2 C:HIS61 4.4 38.0 1.0 CZ C:PHE49 4.5 44.5 1.0 N C:GLY44 4.5 49.4 1.0 CA C:GLY44 4.5 51.3 1.0 N C:ILE42 4.6 56.6 1.0 CE1 C:PHE49 4.7 43.4 1.0 ND2 C:ASN50 5.0 41.4 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