Calcium in PDB 7lz7: Tubulin-RB3_SLD-Ttl in Complex with Compound 5K

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K, PDB code: 7lz7 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)	49.88 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.211, 157.998, 182.056, 90, 90, 90
R / Rfree (%)	17.1 / 21.1

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5K (pdb code 7lz7). 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 5K, PDB code: 7lz7:
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 5K


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 5K within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:62.3 occ:1.00 OD2 A:ASP39 2.3 53.3 1.0 OG1 A:THR41 2.4 93.8 1.0 O A:THR41 2.4 72.7 1.0 OD1 A:ASP39 2.4 54.7 1.0 OE2 A:GLU55 2.4 74.4 1.0 O A:GLY44 2.5 61.5 1.0 OE1 A:GLU55 2.5 69.5 1.0 CG A:ASP39 2.7 53.7 1.0 CD A:GLU55 2.8 69.5 1.0 C A:THR41 3.5 74.1 1.0 C A:GLY44 3.6 64.2 1.0 CB A:THR41 3.6 80.2 1.0 CA A:THR41 4.0 77.5 1.0 CB A:ASP39 4.2 53.2 1.0 N A:THR41 4.2 74.2 1.0 CG A:GLU55 4.3 65.4 1.0 CZ A:PHE49 4.3 63.4 1.0 N A:GLY44 4.4 64.7 1.0 N A:GLY45 4.5 65.6 1.0 NE2 A:HIS61 4.5 65.6 1.0 CA A:GLY45 4.5 66.0 1.0 CA A:GLY44 4.5 63.0 1.0 OD1 A:ASN50 4.6 60.0 1.0 CE1 A:PHE49 4.6 57.3 1.0 N A:ILE42 4.6 72.6 1.0 ND2 A:ASN50 4.7 52.1 1.0 CG2 A:THR41 4.8 71.1 1.0 OD2 A:ASP47 5.0 71.0 1.0

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


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 5K within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:47.7 occ:1.00 OD2 C:ASP39 2.3 51.8 1.0 OE2 C:GLU55 2.4 49.3 1.0 OG1 C:THR41 2.4 58.6 1.0 O C:THR41 2.4 45.3 1.0 O C:HOH605 2.4 40.9 1.0 OE1 C:GLU55 2.4 42.5 1.0 O C:GLY44 2.4 56.6 1.0 OD1 C:ASP39 2.4 52.5 1.0 CG C:ASP39 2.7 49.8 1.0 CD C:GLU55 2.7 45.2 1.0 C C:THR41 3.5 50.0 1.0 C C:GLY44 3.5 52.7 1.0 CB C:THR41 3.6 53.3 1.0 CA C:THR41 3.9 51.3 1.0 CA C:GLY45 4.2 42.3 1.0 N C:THR41 4.2 47.3 1.0 CB C:ASP39 4.2 51.2 1.0 CG C:GLU55 4.2 40.0 1.0 N C:GLY45 4.3 45.8 1.0 O C:HOH612 4.3 47.8 1.0 OD2 C:ASP47 4.4 56.2 1.0 N C:GLY44 4.5 61.9 1.0 OD1 C:ASN50 4.5 38.2 1.0 CA C:GLY44 4.5 56.5 1.0 CZ C:PHE49 4.5 34.4 1.0 N C:ILE42 4.6 56.8 1.0 NE2 C:HIS61 4.7 32.9 1.0 CG2 C:THR41 4.8 48.0 1.0 CE1 C:PHE49 4.9 37.3 1.0 ND2 C:ASN50 5.0 33.1 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