Magnesium in PDB 6bry: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A, PDB code: 6bry 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)	49.75 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.089, 157.766, 181.456, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.6

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A 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 6A (pdb code 6bry). 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 6A, PDB code: 6bry:
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 6A


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 6A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:23.5 occ:1.00 O A:HOH609 1.8 30.6 1.0 O2G A:GTP501 2.0 26.7 1.0 O A:HOH618 2.3 25.6 1.0 O A:HOH629 2.3 29.3 1.0 O2B A:GTP501 2.3 22.2 1.0 O A:HOH603 2.4 39.6 1.0 PG A:GTP501 3.1 41.1 1.0 PB A:GTP501 3.3 40.2 1.0 OE2 A:GLU71 3.5 48.7 1.0 O3B A:GTP501 3.5 33.0 1.0 O3G A:GTP501 3.6 21.7 1.0 O3A A:GTP501 3.7 32.8 1.0 OD2 A:ASP98 3.9 34.7 1.0 OD2 A:ASP69 4.3 37.5 1.0 OD1 A:ASP69 4.3 34.7 1.0 CB A:GLN11 4.3 22.6 1.0 CB A:ASP98 4.3 30.1 1.0 O1G A:GTP501 4.5 21.2 1.0 CG A:ASP98 4.5 33.1 1.0 NZ B:LYS252 4.6 42.7 1.0 O1B A:GTP501 4.6 39.0 1.0 N A:GLN11 4.6 23.3 1.0 OE1 A:GLN11 4.7 30.2 1.0 CD A:GLU71 4.7 48.2 1.0 O2A A:GTP501 4.8 29.1 1.0 CG A:ASP69 4.8 36.7 1.0 PA A:GTP501 4.8 25.1 1.0

Magnesium binding site 2 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A


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 6A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:37.0 occ:1.00 OE1 B:GLN11 2.3 52.1 1.0 O2A B:GDP501 2.5 23.6 1.0 O B:HOH641 2.8 42.1 1.0 CD B:GLN11 3.6 47.0 1.0 OD1 B:ASP177 3.6 64.1 1.0 PA B:GDP501 3.9 17.6 1.0 ND2 B:ASN99 4.2 22.0 1.0 O3A B:GDP501 4.3 24.0 1.0 C5' B:GDP501 4.3 13.2 1.0 NE2 B:GLN11 4.4 47.0 1.0 CG B:ASP177 4.5 58.5 1.0 O5' B:GDP501 4.5 16.5 1.0 CB B:GLN11 4.5 32.7 1.0 OE1 C:GLU254 4.5 49.9 1.0 CG B:GLN11 4.6 40.3 1.0 O2B B:GDP501 4.9 28.4 1.0 O1A B:GDP501 5.0 15.8 1.0

Magnesium binding site 3 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A


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 6A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:40.9 occ:1.00 O C:HOH602 1.8 22.8 1.0 O C:HOH606 1.9 28.4 1.0 O2B C:GTP501 2.0 33.0 1.0 O C:HOH644 2.0 22.2 1.0 O3G C:GTP501 2.2 22.0 1.0 O C:HOH665 2.3 32.0 1.0 PB C:GTP501 3.2 21.0 1.0 PG C:GTP501 3.3 23.3 1.0 OE2 C:GLU71 3.5 42.6 1.0 O3B C:GTP501 3.6 21.1 1.0 OD2 C:ASP69 3.7 22.4 1.0 O3A C:GTP501 3.9 30.1 1.0 O2G C:GTP501 3.9 21.9 1.0 CB C:GLN11 4.0 21.7 1.0 OD1 C:ASP69 4.0 26.6 1.0 N C:GLN11 4.2 21.1 1.0 CG C:ASP69 4.3 28.3 1.0 OD2 C:ASP98 4.4 28.7 1.0 O1B C:GTP501 4.4 20.5 1.0 O1G C:GTP501 4.6 21.7 1.0 O2A C:GTP501 4.6 21.3 1.0 CD C:GLU71 4.7 41.0 1.0 CB C:ASP98 4.7 23.9 1.0 CA C:GLN11 4.7 21.4 1.0 PA C:GTP501 4.8 20.8 1.0 OE1 C:GLN11 4.8 22.9 1.0 OG1 C:THR145 4.9 30.4 1.0 NZ D:LYS252 4.9 44.5 1.0 CG C:ASP98 5.0 28.4 1.0

Magnesium binding site 4 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A


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 6A within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:88.3 occ:1.00 O3G F:ACP402 2.3 0.4 1.0 OE1 F:GLU331 2.3 87.0 1.0 O2B F:ACP402 2.4 0.4 1.0 CD F:GLU331 3.1 84.0 1.0 OE2 F:GLU331 3.3 89.2 1.0 PB F:ACP402 3.5 0.2 1.0 PG F:ACP402 3.5 0.8 1.0 ND2 F:ASN333 3.7 88.9 1.0 C3B F:ACP402 3.8 0.3 1.0 H3B2 F:ACP402 3.8 0.9 1.0 O1B F:ACP402 4.2 0.3 1.0 O1G F:ACP402 4.4 0.4 1.0 CG F:ASN333 4.4 80.6 1.0 CG F:GLU331 4.5 74.8 1.0 O2G F:ACP402 4.6 0.1 1.0 H3B1 F:ACP402 4.7 0.9 1.0 O3A F:ACP402 4.8 0.6 1.0 OD1 F:ASN333 4.9 85.2 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