Magnesium in PDB 6br1: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4A

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4A, PDB code: 6br1 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)	49.64 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.927, 157.613, 180.989, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.5

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4A 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 4A (pdb code 6br1). 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 4A, PDB code: 6br1:
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 4A


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:23.3 occ:1.00 O2G A:GTP501 2.1 22.6 1.0 O A:HOH669 2.1 24.1 1.0 O A:HOH642 2.1 25.3 1.0 O A:HOH631 2.2 23.2 1.0 O A:HOH727 2.2 22.5 1.0 O2B A:GTP501 2.2 23.7 1.0 PG A:GTP501 3.2 29.3 1.0 PB A:GTP501 3.3 25.5 1.0 O3B A:GTP501 3.6 30.9 1.0 O3G A:GTP501 3.7 28.3 1.0 OE2 A:GLU71 3.7 46.6 1.0 O B:HOH605 3.8 51.1 1.0 O3A A:GTP501 3.8 28.5 1.0 OD1 A:ASP69 4.1 31.7 1.0 CB A:GLN11 4.1 23.7 1.0 OD2 A:ASP69 4.1 31.3 1.0 OD2 A:ASP98 4.2 30.8 1.0 CB A:ASP98 4.3 31.6 1.0 N A:GLN11 4.4 24.7 1.0 O1G A:GTP501 4.5 28.1 1.0 CG A:ASP69 4.6 30.4 1.0 O1B A:GTP501 4.6 30.4 1.0 NZ B:LYS252 4.6 57.3 1.0 CG A:ASP98 4.7 30.9 1.0 O2A A:GTP501 4.7 22.4 1.0 OE1 A:GLN11 4.8 32.9 1.0 PA A:GTP501 4.8 26.7 1.0 CA A:GLN11 4.8 27.4 1.0 CD A:GLU71 4.9 45.6 1.0 OG1 A:THR145 5.0 30.0 1.0

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


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:23.1 occ:1.00 OE1 B:GLN11 2.2 32.3 1.0 O2A B:GDP501 2.3 30.2 1.0 O C:HOH742 2.3 39.0 1.0 O B:HOH651 2.3 33.4 1.0 O B:HOH615 2.4 29.2 1.0 O B:HOH684 2.6 30.9 1.0 CD B:GLN11 3.4 39.5 1.0 PA B:GDP501 3.5 25.6 1.0 O3A B:GDP501 3.8 33.6 1.0 OD2 B:ASP177 3.8 34.9 1.0 CB B:GLN11 4.1 31.8 1.0 C5' B:GDP501 4.2 24.8 1.0 O5' B:GDP501 4.3 24.5 1.0 CG B:GLN11 4.3 37.2 1.0 ND2 B:ASN99 4.4 22.7 1.0 NE2 B:GLN11 4.4 35.5 1.0 O C:HOH663 4.6 38.9 1.0 O1A B:GDP501 4.7 23.4 1.0 CG B:ASP177 4.7 36.0 1.0 O2B B:GDP501 4.7 16.3 1.0 C8 B:GDP501 4.8 26.5 1.0 OE1 C:GLU254 4.9 43.1 1.0 PB B:GDP501 4.9 26.2 1.0

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


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:22.9 occ:1.00 O3G C:GTP501 2.1 22.9 1.0 O C:HOH612 2.1 23.2 1.0 O C:HOH787 2.1 23.1 1.0 O C:HOH685 2.1 23.7 1.0 O C:HOH660 2.1 23.0 1.0 O2B C:GTP501 2.2 22.2 1.0 PB C:GTP501 3.2 21.9 1.0 PG C:GTP501 3.3 26.5 1.0 O3B C:GTP501 3.6 28.1 1.0 O3A C:GTP501 3.7 31.6 1.0 OE1 C:GLU71 3.9 44.3 1.0 O2G C:GTP501 3.9 28.8 1.0 CB C:GLN11 4.0 22.4 1.0 OD1 C:ASP69 4.1 23.2 1.0 OD2 C:ASP69 4.2 32.3 1.0 N C:GLN11 4.3 22.0 1.0 OD2 C:ASP98 4.4 33.7 1.0 O1G C:GTP501 4.5 22.7 1.0 O2A C:GTP501 4.5 26.0 1.0 CB C:ASP98 4.5 27.3 1.0 O1B C:GTP501 4.6 21.5 1.0 CG C:ASP69 4.6 28.6 1.0 NZ D:LYS252 4.6 54.5 1.0 OE1 C:GLN11 4.7 25.7 1.0 PA C:GTP501 4.7 21.7 1.0 CA C:GLN11 4.7 27.6 1.0 CG C:ASP98 4.9 32.7 1.0

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


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:71.9 occ:1.00 O2B F:ACP402 2.2 96.8 1.0 OE1 F:GLU331 2.4 79.7 1.0 O3G F:ACP402 2.5 0.8 1.0 NZ F:LYS74 3.0 64.0 1.0 CD F:GLU331 3.3 77.7 1.0 ND2 F:ASN333 3.4 81.7 1.0 OE2 F:GLU331 3.5 83.7 1.0 PB F:ACP402 3.6 95.3 1.0 PG F:ACP402 3.8 0.5 1.0 O1B F:ACP402 4.1 97.2 1.0 O1G F:ACP402 4.3 0.9 1.0 CE F:LYS74 4.4 59.1 1.0 C3B F:ACP402 4.5 0.9 1.0 CG F:ASN333 4.5 76.9 1.0 CG F:GLU331 4.7 69.8 1.0 O3A F:ACP402 4.8 90.5 1.0 OD1 F:ASN333 4.8 83.9 1.0 O2G F:ACP402 5.0 0.1 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