Magnesium in PDB 6brf: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B, PDB code: 6brf 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)	49.78 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.129, 157.747, 181.596, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.7

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B (pdb code 6brf). 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 Heterocyclic Pyrimidine Compound 4B, PDB code: 6brf:
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 Heterocyclic Pyrimidine Compound 4B


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 Heterocyclic Pyrimidine Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:26.7 occ:1.00 O A:HOH644 2.0 29.4 1.0 O2G A:GTP501 2.1 27.0 1.0 O A:HOH610 2.1 26.2 1.0 O A:HOH654 2.1 26.6 1.0 O A:HOH601 2.2 43.5 1.0 O2B A:GTP501 2.3 25.7 1.0 PG A:GTP501 3.3 31.8 1.0 OE2 A:GLU71 3.3 50.3 1.0 PB A:GTP501 3.3 29.5 1.0 O3B A:GTP501 3.6 36.6 1.0 O3G A:GTP501 3.8 27.2 1.0 O3A A:GTP501 3.9 31.0 1.0 CB A:GLN11 4.1 28.2 1.0 OD2 A:ASP98 4.1 36.6 1.0 OD2 A:ASP69 4.2 30.3 1.0 OD1 A:ASP69 4.2 27.8 1.0 CB A:ASP98 4.4 38.1 1.0 OE1 A:GLN11 4.4 34.3 1.0 N A:GLN11 4.4 26.9 1.0 O2A A:GTP501 4.5 29.9 1.0 CD A:GLU71 4.5 48.8 1.0 O1G A:GTP501 4.5 28.7 1.0 O1B A:GTP501 4.6 32.8 1.0 CG A:ASP98 4.6 37.6 1.0 CG A:ASP69 4.7 31.8 1.0 PA A:GTP501 4.8 34.7 1.0 CA A:GLN11 4.9 28.8 1.0 OE1 A:GLU71 5.0 52.7 1.0

Magnesium binding site 2 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B


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 Heterocyclic Pyrimidine Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:26.0 occ:1.00 O B:HOH606 2.0 27.7 1.0 O B:HOH615 2.1 28.8 1.0 OE1 B:GLN11 2.2 39.5 1.0 O2A B:GDP501 2.2 26.7 1.0 O C:HOH742 2.3 24.8 1.0 O B:HOH669 2.3 36.5 1.0 CD B:GLN11 3.4 43.0 1.0 PA B:GDP501 3.5 23.2 1.0 O3A B:GDP501 3.7 21.5 1.0 OD2 B:ASP177 3.8 43.4 1.0 CB B:GLN11 4.0 28.6 1.0 ND2 B:ASN99 4.3 30.2 1.0 CG B:GLN11 4.3 36.0 1.0 C5' B:GDP501 4.3 19.1 1.0 O5' B:GDP501 4.3 17.7 1.0 O2B B:GDP501 4.4 18.4 1.0 NE2 B:GLN11 4.4 47.3 1.0 O C:HOH621 4.4 47.7 1.0 O1A B:GDP501 4.6 20.9 1.0 PB B:GDP501 4.7 37.8 1.0 OE1 C:GLU254 4.7 37.9 1.0 CG B:ASP177 4.9 39.4 1.0 C8 B:GDP501 5.0 30.2 1.0

Magnesium binding site 3 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B


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 Heterocyclic Pyrimidine Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:25.8 occ:1.00 O C:HOH691 1.9 27.6 1.0 O3G C:GTP501 2.0 25.7 1.0 O C:HOH658 2.0 25.8 1.0 O C:HOH655 2.0 26.6 1.0 O C:HOH616 2.2 26.1 1.0 O2B C:GTP501 2.2 25.0 1.0 PG C:GTP501 3.1 26.6 1.0 PB C:GTP501 3.2 24.7 1.0 O3B C:GTP501 3.4 27.6 1.0 O2G C:GTP501 3.6 25.6 1.0 OE1 C:GLU71 3.6 49.7 1.0 O3A C:GTP501 3.7 28.2 1.0 OD1 C:ASP69 4.1 29.0 1.0 OD2 C:ASP69 4.1 26.0 1.0 CB C:ASP98 4.3 29.7 1.0 NZ D:LYS252 4.3 45.7 1.0 CB C:GLN11 4.3 25.4 1.0 OD2 C:ASP98 4.3 38.0 1.0 O1G C:GTP501 4.3 26.9 1.0 N C:GLN11 4.5 24.8 1.0 O1B C:GTP501 4.5 24.3 1.0 CG C:ASP69 4.5 30.5 1.0 O2A C:GTP501 4.7 30.4 1.0 CG C:ASP98 4.7 33.6 1.0 OE1 C:GLN11 4.8 31.3 1.0 CD C:GLU71 4.8 46.5 1.0 PA C:GTP501 4.8 31.2 1.0 OG1 C:THR145 4.8 25.1 1.0 CA C:GLN11 5.0 28.3 1.0

Magnesium binding site 4 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B


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 Heterocyclic Pyrimidine Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:0.2 occ:1.00 H3B2 F:ACP402 1.9 0.5 1.0 OE1 F:GLU331 2.2 0.5 1.0 O3G F:ACP402 2.3 0.7 1.0 C3B F:ACP402 2.6 0.1 1.0 PG F:ACP402 2.8 0.6 1.0 H3B1 F:ACP402 3.1 0.5 1.0 CD F:GLU331 3.3 0.1 1.0 O1G F:ACP402 3.4 0.0 1.0 CG F:GLU331 4.0 92.8 1.0 PB F:ACP402 4.1 0.6 1.0 OE2 F:GLU331 4.1 0.6 1.0 O2G F:ACP402 4.2 0.6 1.0 O3A F:ACP402 4.4 0.4 1.0 O1B F:ACP402 4.7 0.2 1.0

S.Banerjee, K.E.Arnst, Y.Wang, G.Kumar, S.Deng, L.Yang, G.B.Li, J.Yang, S.W.White, W.Li, D.D.Miller. Heterocyclic-Fused Pyrimidines As Novel Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site: Structural Basis and Antitumor Efficacy. J. Med. Chem. V. 61 1704 2018.
ISSN: ISSN 1520-4804
PubMed: 29406710
DOI: 10.1021/ACS.JMEDCHEM.7B01858