Calcium in PDB 6x1f: Tubulin-RB3_SLD-Ttl in Complex with Compound 5M

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5M, PDB code: 6x1f was solved by S.W.White, M.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.24 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.48, 157.923, 182.205, 90, 90, 90
R / Rfree (%)	19 / 24.1

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5M 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 5M (pdb code 6x1f). 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 5M, PDB code: 6x1f:
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 5M


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 5M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:66.5 occ:1.00 O A:HOH635 2.3 60.4 1.0 OD2 A:ASP39 2.3 56.1 1.0 O A:THR41 2.3 67.8 1.0 O A:GLY44 2.3 60.4 1.0 OE1 A:GLU55 2.4 68.4 1.0 OD1 A:ASP39 2.4 60.3 1.0 OG1 A:THR41 2.4 71.9 1.0 OE2 A:GLU55 2.4 72.7 1.0 CG A:ASP39 2.7 56.8 1.0 CD A:GLU55 2.7 67.9 1.0 C A:THR41 3.4 70.7 1.0 CB A:THR41 3.5 70.9 1.0 C A:GLY44 3.5 69.3 1.0 CA A:THR41 3.9 71.3 1.0 N A:THR41 4.2 68.6 1.0 CB A:ASP39 4.2 59.6 1.0 CG A:GLU55 4.3 62.4 1.0 N A:GLY44 4.3 66.4 1.0 N A:GLY45 4.4 71.6 1.0 CZ A:PHE49 4.4 57.2 1.0 CA A:GLY44 4.4 68.5 1.0 CA A:GLY45 4.5 71.6 1.0 N A:ILE42 4.6 72.0 1.0 OD2 A:ASP47 4.6 61.3 1.0 OD1 A:ASN50 4.7 55.4 1.0 CG2 A:THR41 4.8 70.0 1.0 NE2 A:HIS61 4.8 57.0 1.0 ND2 A:ASN50 4.8 50.2 1.0 CE1 A:PHE49 4.9 54.0 1.0 CA A:ILE42 5.0 71.8 1.0

Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5M


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 5M within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:49.5 occ:1.00 OD2 C:ASP39 2.3 51.1 1.0 OE2 C:GLU55 2.4 45.5 1.0 O C:THR41 2.4 49.7 1.0 OG1 C:THR41 2.4 55.2 1.0 OE1 C:GLU55 2.4 43.9 1.0 O C:HOH608 2.4 39.1 1.0 OD1 C:ASP39 2.4 51.8 1.0 O C:GLY44 2.5 51.2 1.0 CD C:GLU55 2.7 43.8 1.0 CG C:ASP39 2.7 51.0 1.0 C C:THR41 3.4 49.9 1.0 CB C:THR41 3.5 49.2 1.0 C C:GLY44 3.5 49.2 1.0 CA C:THR41 3.9 48.2 1.0 CA C:GLY45 4.1 46.2 1.0 N C:THR41 4.1 46.1 1.0 N C:GLY45 4.2 45.3 1.0 CG C:GLU55 4.2 39.5 1.0 CB C:ASP39 4.2 54.5 1.0 O C:HOH632 4.4 45.9 1.0 OD2 C:ASP47 4.4 43.0 1.0 CA C:GLY44 4.5 53.1 1.0 N C:GLY44 4.5 55.2 1.0 NE2 C:HIS61 4.6 34.4 1.0 N C:ILE42 4.6 60.2 1.0 OD1 C:ASN50 4.6 40.6 1.0 CZ C:PHE49 4.6 32.7 1.0 CG2 C:THR41 4.8 44.3 1.0 CE1 C:PHE49 4.9 33.1 1.0 ND2 C:ASN50 4.9 36.3 1.0

S.Banerjee, F.Mahmud, S.Deng, L.Ma, M.K.Yun, S.O.Fakayode, K.E.Arnst, L.Yang, H.Chen, Z.Wu, P.B.Lukka, K.Parmar, B.Meibohm, S.W.White, Y.Wang, W.Li, D.D.Miller. X-Ray Crystallography-Guided Design, Antitumor Efficacy, and Qsar Analysis of Metabolically Stable Cyclopenta-Pyrimidinyl Dihydroquinoxalinone As A Potent Tubulin Polymerization Inhibitor. J.Med.Chem. V. 64 13072 2021.
ISSN: ISSN 0022-2623
PubMed: 34406768
DOI: 10.1021/ACS.JMEDCHEM.1C01202