Calcium in PDB 6pc4: Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-274

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-274, PDB code: 6pc4 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)	41.74 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.143, 157.533, 181.961, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.4

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-274 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-274 (pdb code 6pc4). 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-274, PDB code: 6pc4:
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-274


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-274 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:60.9 occ:1.00 OE1 A:GLU55 2.4 66.1 1.0 O A:THR41 2.4 71.4 1.0 O A:GLY44 2.5 71.8 1.0 OD1 A:ASP39 2.5 63.6 1.0 OD2 A:ASP39 2.5 63.0 1.0 OG1 A:THR41 2.7 65.6 1.0 CG A:ASP39 2.8 63.6 1.0 OE2 A:GLU55 2.9 69.7 1.0 CD A:GLU55 3.0 67.2 1.0 C A:THR41 3.4 71.7 1.0 C A:GLY44 3.5 67.5 1.0 CB A:THR41 3.5 67.7 1.0 CA A:THR41 3.9 71.4 1.0 N A:THR41 4.2 72.5 1.0 N A:GLY45 4.2 66.0 1.0 CA A:GLY45 4.3 68.2 1.0 N A:GLY44 4.3 70.3 1.0 CB A:ASP39 4.3 62.9 1.0 CA A:GLY44 4.4 68.9 1.0 CG A:GLU55 4.4 64.2 1.0 OD1 A:ASN50 4.5 52.4 1.0 CZ A:PHE49 4.6 57.5 1.0 OD1 A:ASP47 4.6 68.7 1.0 N A:ILE42 4.6 71.8 1.0 NE2 A:HIS61 4.6 63.5 1.0 ND2 A:ASN50 4.8 51.0 1.0 CG2 A:THR41 4.9 64.0 1.0

Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-274


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-274 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:46.0 occ:1.00 OE2 C:GLU55 2.3 40.1 1.0 O C:THR41 2.4 53.1 1.0 OG1 C:THR41 2.5 53.5 1.0 OD2 C:ASP39 2.5 59.5 1.0 OD1 C:ASP39 2.5 57.7 1.0 O C:HOH604 2.5 31.9 1.0 O C:GLY44 2.6 58.2 1.0 OE1 C:GLU55 2.7 43.0 1.0 CD C:GLU55 2.8 40.6 1.0 CG C:ASP39 2.9 58.4 1.0 C C:THR41 3.4 51.5 1.0 CB C:THR41 3.4 49.0 1.0 C C:GLY44 3.5 56.7 1.0 CA C:THR41 3.8 49.2 1.0 N C:THR41 4.1 46.6 1.0 N C:GLY45 4.3 52.8 1.0 CA C:GLY45 4.3 51.1 1.0 CG C:GLU55 4.3 34.6 1.0 N C:GLY44 4.3 58.8 1.0 CB C:ASP39 4.4 59.4 1.0 OD2 C:ASP47 4.4 52.3 1.0 CA C:GLY44 4.5 57.2 1.0 OD1 C:ASN50 4.5 39.2 1.0 N C:ILE42 4.6 51.5 1.0 CZ C:PHE49 4.7 43.5 1.0 NE2 C:HIS61 4.7 35.0 1.0 CG2 C:THR41 4.7 41.8 1.0 CE1 C:PHE49 4.9 42.2 1.0 ND2 C:ASN50 5.0 27.4 1.0 O C:HOH679 5.0 37.5 1.0

H.Chen, S.Deng, Y.Wang, N.Albadari, G.Kumar, D.Ma, W.Li, S.W.White, D.D.Miller, W.Li. Structure-Activity Relationship Study of Novel 6-Aryl-2-Benzoyl-Pyridines As Tubulin Polymerization Inhibitors with Potent Antiproliferative Properties. J.Med.Chem. V. 63 827 2020.
ISSN: ISSN 0022-2623
PubMed: 31860298
DOI: 10.1021/ACS.JMEDCHEM.9B01815