Magnesium in PDB 6bs2: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B, PDB code: 6bs2 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 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.101, 157.602, 181.509, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.4

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B (pdb code 6bs2). 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 8B, PDB code: 6bs2:
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 8B


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 8B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:18.1 occ:1.00 O A:HOH610 2.1 20.0 1.0 O2G A:GTP501 2.1 26.8 1.0 O2B A:GTP501 2.2 23.3 1.0 O A:HOH609 2.2 21.3 1.0 O A:HOH624 2.2 24.1 1.0 O A:HOH605 2.2 27.9 1.0 PG A:GTP501 3.1 25.6 1.0 PB A:GTP501 3.2 29.2 1.0 O3B A:GTP501 3.5 29.2 1.0 O3G A:GTP501 3.6 24.6 1.0 O3A A:GTP501 3.7 27.6 1.0 OE2 A:GLU71 3.8 43.9 1.0 OD2 A:ASP98 4.1 40.9 1.0 CB A:GLN11 4.1 24.5 1.0 OD1 A:ASP69 4.4 34.9 1.0 OD2 A:ASP69 4.4 32.9 1.0 CB A:ASP98 4.4 33.8 1.0 O1G A:GTP501 4.4 25.4 1.0 N A:GLN11 4.5 25.4 1.0 O1B A:GTP501 4.5 24.2 1.0 CG A:ASP98 4.6 39.2 1.0 O2A A:GTP501 4.6 23.0 1.0 PA A:GTP501 4.7 22.9 1.0 CG A:ASP69 4.8 32.8 1.0 CA A:GLN11 4.9 29.7 1.0 OG1 A:THR145 5.0 26.9 1.0

Magnesium binding site 2 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B


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 8B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:22.0 occ:1.00 OE1 B:GLN11 2.1 43.0 1.0 O B:HOH602 2.2 17.6 1.0 O C:HOH649 2.3 45.2 1.0 O2A B:GDP501 2.3 19.8 1.0 O B:HOH624 2.3 28.4 1.0 OD2 B:ASP177 3.2 51.6 1.0 CD B:GLN11 3.3 40.2 1.0 PA B:GDP501 3.6 22.1 1.0 CB B:GLN11 4.0 28.6 1.0 O3A B:GDP501 4.1 19.1 1.0 CG B:GLN11 4.2 35.8 1.0 NE2 B:GLN11 4.3 40.0 1.0 C5' B:GDP501 4.3 19.1 1.0 CG B:ASP177 4.4 48.1 1.0 O5' B:GDP501 4.4 18.4 1.0 OD1 B:ASN99 4.4 25.4 1.0 O2B B:GDP501 4.6 19.5 1.0 C8 B:GDP501 4.7 24.4 1.0 O1A B:GDP501 4.7 18.8 1.0

Magnesium binding site 3 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B


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 8B within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg504 b:18.2 occ:1.00 O3G C:GTP501 1.9 25.0 1.0 O C:HOH606 2.1 21.3 1.0 O C:HOH605 2.1 8.6 1.0 O C:HOH608 2.2 15.1 1.0 O2B C:GTP501 2.6 18.5 1.0 PG C:GTP501 3.2 23.1 1.0 OE1 C:GLU71 3.5 38.1 1.0 OD2 C:ASP98 3.5 44.9 1.0 O2G C:GTP501 3.7 24.6 1.0 NZ D:LYS252 3.7 46.3 1.0 PB C:GTP501 3.7 21.7 1.0 O3B C:GTP501 3.9 25.5 1.0 CB C:ASP98 4.0 33.8 1.0 CG C:ASP98 4.1 43.4 1.0 O3A C:GTP501 4.2 24.6 1.0 O1G C:GTP501 4.4 26.6 1.0 OD1 C:ASP69 4.5 23.7 1.0 OD2 C:ASP69 4.5 24.0 1.0 CD C:GLU71 4.6 39.1 1.0 OD1 D:ASN247 4.6 0.0 1.0 CB C:GLN11 4.7 18.7 1.0 NE2 C:GLN11 4.7 23.1 1.0 CE D:LYS252 4.8 40.7 1.0 O2A C:GTP501 4.9 25.4 1.0 CG C:ASP69 5.0 24.5 1.0 CB C:GLU71 5.0 28.8 1.0

Magnesium binding site 4 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B


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 8B within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:59.1 occ:1.00 O3G F:ACP402 2.4 93.2 1.0 OE2 F:GLU331 2.5 90.0 1.0 O2B F:ACP402 3.0 90.0 1.0 ND2 F:ASN333 3.1 81.3 1.0 CD F:GLU331 3.3 87.5 1.0 NZ F:LYS74 3.4 67.2 1.0 OE1 F:GLU331 3.6 89.7 1.0 PG F:ACP402 3.8 89.3 1.0 H3B2 F:ACP402 4.0 0.2 1.0 PB F:ACP402 4.0 94.5 1.0 C3B F:ACP402 4.1 90.9 1.0 CG F:ASN333 4.2 75.0 1.0 CG F:GLU331 4.5 81.3 1.0 O3A F:ACP402 4.6 87.2 1.0 O1G F:ACP402 4.7 88.0 1.0 CE F:LYS74 4.8 65.7 1.0 O2G F:ACP402 4.8 87.4 1.0 OD1 F:ASN333 4.8 76.8 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