Calcium in PDB 7lz8: Tubulin-RB3_SLD-Ttl in Complex with Compound 5T

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5T, PDB code: 7lz8 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)	45.36 / 2.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.57, 155.041, 182.339, 90, 90, 90
R / Rfree (%)	18.4 / 22.8

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

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	4 atoms

The binding sites of Calcium atom in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5T (pdb code 7lz8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5T, PDB code: 7lz8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5T


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 5T within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:133.9 occ:1.00 OE2 A:GLU55 2.4 124.4 1.0 OG1 A:THR41 2.4 145.2 1.0 OE1 A:GLU55 2.4 121.7 1.0 OD1 A:ASP39 2.5 113.8 1.0 O A:GLY44 2.6 110.8 1.0 O A:THR41 2.7 123.2 1.0 CD A:GLU55 2.7 115.9 1.0 OD2 A:ASP39 2.7 112.2 1.0 CG A:ASP39 3.0 108.9 1.0 CB A:THR41 3.2 127.2 1.0 C A:THR41 3.6 119.2 1.0 C A:GLY44 3.7 117.8 1.0 CA A:THR41 3.9 122.4 1.0 OD1 A:ASN50 4.0 117.7 1.0 CG A:GLU55 4.2 107.5 1.0 CZ A:PHE49 4.2 95.9 1.0 CA A:GLY45 4.4 143.4 1.0 N A:GLY45 4.4 133.5 1.0 CB A:ASP39 4.4 106.5 1.0 CG2 A:THR41 4.4 115.7 1.0 N A:THR41 4.5 121.4 1.0 ND2 A:ASN50 4.5 94.2 1.0 N A:GLY44 4.5 117.0 1.0 OD1 A:ASP47 4.5 114.2 1.0 NE2 A:HIS61 4.5 99.1 1.0 CA A:GLY44 4.7 110.9 1.0 CG A:ASN50 4.7 103.6 1.0 CE1 A:PHE49 4.7 102.9 1.0 N A:ILE42 4.8 115.8 1.0

Calcium binding site 2 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5T


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 5T within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:120.2 occ:1.00 OD2 B:ASP118 3.7 107.2 1.0 OD1 B:ASP118 4.4 109.5 1.0 CG B:ASP118 4.5 99.6 1.0

Calcium binding site 3 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5T


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-RB3_SLD-Ttl in Complex with Compound 5T within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:97.2 occ:1.00 OD2 C:ASP39 2.2 82.9 1.0 OG1 C:THR41 2.3 107.8 1.0 OE2 C:GLU55 2.3 106.1 1.0 O C:THR41 2.4 101.0 1.0 OE1 C:GLU55 2.4 106.4 1.0 OD1 C:ASP39 2.5 85.2 1.0 O C:GLY44 2.6 85.4 1.0 CD C:GLU55 2.7 96.7 1.0 CG C:ASP39 2.7 77.8 1.0 C C:THR41 3.4 97.9 1.0 CB C:THR41 3.4 92.1 1.0 C C:GLY44 3.6 87.6 1.0 CA C:THR41 3.8 92.6 1.0 CA C:GLY45 4.0 91.2 1.0 OD2 C:ASP47 4.0 98.2 1.0 N C:THR41 4.2 92.5 1.0 N C:GLY45 4.2 90.1 1.0 CG C:GLU55 4.2 73.1 1.0 CB C:ASP39 4.2 82.1 1.0 CZ C:PHE49 4.5 72.8 1.0 N C:ILE42 4.5 100.5 1.0 OD1 C:ASN50 4.7 72.8 1.0 N C:GLY44 4.7 92.7 1.0 CG2 C:THR41 4.7 74.2 1.0 NE2 C:HIS61 4.7 78.8 1.0 CA C:GLY44 4.8 88.4 1.0 CE1 C:PHE49 4.8 69.0 1.0 CA C:ILE42 5.0 99.9 1.0 ND2 C:ASN50 5.0 61.0 1.0

Calcium binding site 4 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5T


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-RB3_SLD-Ttl in Complex with Compound 5T within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:124.3 occ:1.00 OD1 C:ASP199 2.4 99.9 1.0 O C:HOH614 2.5 117.2 1.0 O C:HOH613 2.5 70.1 1.0 CG C:ASP199 3.5 82.0 1.0 OD2 C:ASP199 3.8 95.6 1.0 O C:GLU196 4.6 57.8 1.0 O C:LYS163 4.7 106.6 1.0 CB C:ASP199 4.7 66.8 1.0 CB C:LYS163 4.8 83.4 1.0 O C:HIS197 4.8 59.9 1.0 CA C:LYS163 4.8 86.8 1.0 CD C:LYS163 4.9 79.3 1.0 C C:HIS197 4.9 53.5 1.0 CE2 E:PHE93 4.9 61.5 1.0 C C:SER198 5.0 49.2 1.0 N C:ASP199 5.0 53.0 1.0 CZ E:PHE93 5.0 68.5 1.0 CG C:LYS163 5.0 71.6 1.0 O C:SER198 5.0 63.7 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