Magnesium in PDB 6nng: Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95, PDB code: 6nng 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)	48.25 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.418, 157.979, 182.840, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.7

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95 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 Compound DJ95 (pdb code 6nng). 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 DJ95, PDB code: 6nng:
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 DJ95


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 DJ95 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:26.8 occ:1.00 O2G A:GTP501 2.1 26.1 1.0 O A:HOH633 2.1 27.8 1.0 O A:HOH668 2.1 30.5 1.0 O A:HOH605 2.2 31.7 1.0 O A:HOH701 2.2 26.0 1.0 O1B A:GTP501 2.4 27.2 1.0 PG A:GTP501 3.3 29.8 1.0 PB A:GTP501 3.5 31.0 1.0 O3G A:GTP501 3.7 33.5 1.0 OE2 A:GLU71 3.8 58.1 1.0 O3B A:GTP501 3.8 42.0 1.0 NZ B:LYS252 3.9 43.0 1.0 O3A A:GTP501 3.9 32.9 1.0 OD2 A:ASP98 4.1 37.6 1.0 OD1 A:ASP69 4.1 40.4 1.0 CB A:GLN11 4.2 30.4 1.0 OD2 A:ASP69 4.2 39.6 1.0 CB A:ASP98 4.4 32.6 1.0 O2A A:GTP501 4.5 34.5 1.0 O1G A:GTP501 4.5 25.7 1.0 N A:GLN11 4.6 29.2 1.0 OE1 A:GLN11 4.6 38.2 1.0 CG A:ASP98 4.6 33.8 1.0 CG A:ASP69 4.6 39.7 1.0 O2B A:GTP501 4.8 40.9 1.0 CD A:GLU71 4.8 56.3 1.0 PA A:GTP501 4.9 30.6 1.0 CA A:GLN11 5.0 33.9 1.0

Magnesium binding site 2 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95


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 DJ95 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:33.8 occ:1.00 O2A B:GDP501 2.2 30.4 1.0 O B:HOH650 2.2 49.4 1.0 O B:HOH627 2.3 41.0 1.0 NE2 B:GLN11 2.5 56.5 1.0 O C:HOH708 2.6 34.9 1.0 O B:HOH649 2.6 37.4 1.0 O B:HOH624 2.6 32.1 1.0 CD B:GLN11 3.5 54.0 1.0 PA B:GDP501 3.6 24.6 1.0 OD2 B:ASP177 3.8 45.8 1.0 O3A B:GDP501 4.1 22.2 1.0 CB B:GLN11 4.2 31.0 1.0 OE1 B:GLN11 4.2 56.1 1.0 CG B:GLN11 4.3 41.3 1.0 C5' B:GDP501 4.3 21.1 1.0 OD1 B:ASN99 4.4 36.9 1.0 O5' B:GDP501 4.5 22.2 1.0 O1A B:GDP501 4.6 24.4 1.0 O3B B:GDP501 4.7 23.3 1.0 CG B:ASP177 4.9 49.8 1.0 OE1 C:GLU254 4.9 46.9 1.0 C8 B:GDP501 4.9 32.3 1.0 PB B:GDP501 5.0 25.3 1.0

Magnesium binding site 3 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95


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 DJ95 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:26.9 occ:1.00 O C:HOH646 2.1 29.4 1.0 O2B C:GTP501 2.1 26.1 1.0 O C:HOH676 2.1 26.9 1.0 O C:HOH748 2.1 26.9 1.0 O C:HOH614 2.2 27.3 1.0 O3G C:GTP501 2.2 26.8 1.0 PB C:GTP501 3.2 25.7 1.0 PG C:GTP501 3.3 27.9 1.0 O3B C:GTP501 3.6 28.7 1.0 O2G C:GTP501 3.7 31.5 1.0 OE1 C:GLU71 3.8 47.9 1.0 O3A C:GTP501 3.8 30.4 1.0 NZ D:LYS252 4.0 27.6 1.0 OD1 C:ASP69 4.0 26.8 1.0 OD2 C:ASP69 4.1 27.1 1.0 CB C:GLN11 4.2 26.5 1.0 N C:GLN11 4.4 25.8 1.0 OD2 C:ASP98 4.5 40.3 1.0 CG C:ASP69 4.5 30.4 1.0 CB C:ASP98 4.5 30.4 1.0 O C:HOH675 4.5 48.0 1.0 O1B C:GTP501 4.5 25.9 1.0 O1G C:GTP501 4.6 26.6 1.0 O2A C:GTP501 4.6 28.2 1.0 OE1 C:GLN11 4.7 37.8 1.0 PA C:GTP501 4.8 25.6 1.0 CG C:ASP98 4.8 35.3 1.0 CA C:GLN11 4.9 31.5 1.0 CD C:GLU71 4.9 47.7 1.0

Magnesium binding site 4 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95


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 DJ95 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:68.5 occ:1.00 O1B F:ACP402 2.3 0.8 1.0 OE1 F:GLU331 2.5 84.2 1.0 O2G F:ACP402 3.3 0.9 1.0 CD F:GLU331 3.3 78.8 1.0 OE2 F:GLU331 3.3 83.1 1.0 PB F:ACP402 3.6 0.2 1.0 NZ F:LYS74 3.7 73.8 1.0 ND2 F:ASN333 3.9 77.1 1.0 O1G F:ACP402 3.9 0.3 1.0 PG F:ACP402 4.0 0.1 1.0 O2B F:ACP402 4.2 0.6 1.0 C3B F:ACP402 4.2 0.5 1.0 CG F:GLU331 4.7 69.2 1.0 O3A F:ACP402 4.9 0.1 1.0 CG F:ASN333 4.9 70.9 1.0 O1A F:ACP402 5.0 0.9 1.0

K.E.Arnst, Y.Wang, Z.N.Lei, D.J.Hwang, G.Kumar, D.Ma, D.N.Parke, Q.Chen, J.Yang, S.W.White, T.N.Seagroves, Z.S.Chen, D.D.Miller, W.Li. Colchicine Binding Site Agent DJ95 Overcomes Drug Resistance and Exhibits Antitumor Efficacy. Mol.Pharmacol. V. 96 73 2019.
ISSN: ESSN 1521-0111
PubMed: 31043459
DOI: 10.1124/MOL.118.114801