Magnesium 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:

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5T, PDB code: 7lz8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg503 b:58.4 occ:1.00 O2G A:GTP501 2.0 57.2 1.0 O A:HOH601 2.1 59.1 1.0 O A:HOH606 2.1 62.9 1.0 O2B A:GTP501 2.1 58.8 1.0 O A:HOH604 2.2 64.7 1.0 O A:HOH605 2.2 66.8 1.0 PB A:GTP501 3.2 59.6 1.0 PG A:GTP501 3.2 67.5 1.0 O3A A:GTP501 3.5 73.5 1.0 O3B A:GTP501 3.6 83.3 1.0 O3G A:GTP501 3.8 58.2 1.0 CB A:GLN11 4.1 61.4 1.0 O2A A:GTP501 4.2 75.1 1.0 OE1 A:GLN11 4.2 64.8 1.0 OE2 A:GLU71 4.3 93.4 1.0 O1G A:GTP501 4.4 56.7 1.0 PA A:GTP501 4.4 57.4 1.0 OD1 A:ASP69 4.5 74.1 1.0 O1B A:GTP501 4.5 76.3 1.0 N A:GLN11 4.5 61.1 1.0 OD2 A:ASP69 4.7 68.3 1.0 OD2 A:ASP98 4.7 71.8 1.0 CB A:ASP98 4.9 64.5 1.0 CA A:GLN11 4.9 60.2 1.0 CG A:ASP98 5.0 69.7 1.0 CD A:GLN11 5.0 61.5 1.0 O1A A:GTP501 5.0 73.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg504 b:109.7 occ:1.00 O B:HOH601 2.1 74.7 1.0 O B:HOH604 2.1 88.6 1.0 OE1 B:GLN11 2.2 78.5 1.0 O B:HOH605 2.3 65.2 1.0 O B:HOH606 2.3 72.9 1.0 O C:HOH604 2.4 65.8 1.0 O2A B:GDP501 3.4 74.4 1.0 CD B:GLN11 3.5 78.8 1.0 CB B:GLN11 4.3 61.4 1.0 NE2 B:GLN11 4.3 98.1 1.0 OD2 B:ASP177 4.3 97.6 1.0 CG B:GLN11 4.4 65.3 1.0 O3A B:GDP501 4.5 51.5 1.0 PA B:GDP501 4.6 47.6 1.0 OE1 C:GLU254 4.7 112.1 1.0 ND2 B:ASN99 4.8 69.9 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg503 b:62.8 occ:1.00 O2B C:GTP501 1.9 77.9 1.0 O C:HOH607 2.0 77.9 1.0 O C:HOH605 2.0 56.3 1.0 O3G C:GTP501 2.1 63.8 1.0 O C:HOH601 2.2 55.9 1.0 O C:HOH609 2.2 69.9 1.0 PB C:GTP501 3.1 58.3 1.0 PG C:GTP501 3.3 55.5 1.0 O3B C:GTP501 3.6 72.2 1.0 O3A C:GTP501 3.6 71.2 1.0 OE1 C:GLU71 3.8 103.7 1.0 O2G C:GTP501 3.9 55.7 1.0 CB C:GLN11 4.3 55.6 1.0 OD1 C:ASP69 4.4 58.8 1.0 O1B C:GTP501 4.4 62.4 1.0 O2A C:GTP501 4.4 55.2 1.0 OD2 C:ASP98 4.4 81.3 1.0 O1G C:GTP501 4.5 55.5 1.0 PA C:GTP501 4.5 54.6 1.0 NE2 C:GLN11 4.6 57.4 1.0 OD2 C:ASP69 4.6 62.5 1.0 N C:GLN11 4.6 54.9 1.0 NZ D:LYS252 4.7 98.9 1.0 CB C:ASP98 4.8 57.2 1.0 CD C:GLU71 4.8 94.0 1.0 CG C:ASP69 4.9 70.8 1.0 O1A C:GTP501 4.9 54.4 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 D:Mg502 b:104.9 occ:1.00 O2G D:GTP501 2.2 116.0 1.0 O D:HOH602 2.2 115.3 1.0 O D:HOH601 2.3 88.0 1.0 O1B D:GTP501 2.5 108.7 1.0 O1G D:GTP501 2.6 83.8 1.0 PG D:GTP501 2.8 113.8 1.0 OD2 D:ASP67 3.3 77.8 1.0 PB D:GTP501 3.4 98.7 1.0 O3B D:GTP501 3.5 110.4 1.0 OD1 D:ASP67 3.7 86.8 1.0 O3A D:GTP501 3.8 105.8 1.0 CG D:ASP67 3.9 87.6 1.0 O3G D:GTP501 4.1 104.9 1.0 N D:GLN11 4.2 98.1 1.0 CB D:GLN11 4.2 112.0 1.0 CB D:GLU69 4.4 106.5 1.0 OE1 D:GLN11 4.7 119.1 1.0 PA D:GTP501 4.8 99.8 1.0 O2B D:GTP501 4.8 115.2 1.0 O2A D:GTP501 4.8 120.8 1.0 CA D:GLN11 4.9 105.8 1.0 OG1 D:THR143 5.0 89.5 1.0 CA D:GLY10 5.0 93.7 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