Magnesium in PDB 6n47: The Structure of Sb-2-204-Tubulin Complex

The structure of The Structure of Sb-2-204-Tubulin Complex, PDB code: 6n47 was solved by K.Arnst, S.Banerjee, Y.Wang, W.Li, D.Miller, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.295, 157.835, 182.068, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.6

The structure of The Structure of Sb-2-204-Tubulin Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium atom in the The Structure of Sb-2-204-Tubulin Complex (pdb code 6n47). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Structure of Sb-2-204-Tubulin Complex, PDB code: 6n47:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:29.9 occ:1.00 O A:HOH610 1.8 30.2 1.0 O1G A:GTP501 1.9 20.3 1.0 O1B A:GTP501 2.0 21.4 1.0 O A:HOH620 2.1 17.9 1.0 O A:HOH629 2.1 19.1 1.0 O A:HOH614 2.1 20.9 1.0 PG A:GTP501 2.9 24.6 1.0 PB A:GTP501 3.0 24.1 1.0 O3B A:GTP501 3.1 26.6 1.0 O2G A:GTP501 3.6 23.9 1.0 O3A A:GTP501 3.6 24.1 1.0 OE2 A:GLU71 4.1 39.9 1.0 OD2 A:ASP98 4.1 29.5 1.0 NZ B:LYS252 4.2 53.2 1.0 OD1 A:ASP69 4.2 31.2 1.0 O3G A:GTP501 4.2 22.4 1.0 O1A A:GTP501 4.3 24.5 1.0 O2B A:GTP501 4.3 27.2 1.0 OD2 A:ASP69 4.3 31.6 1.0 CB A:GLN11 4.4 26.4 1.0 N A:GLN11 4.4 26.7 1.0 PA A:GTP501 4.6 23.6 1.0 CB A:ASP98 4.6 32.9 1.0 CG A:ASP98 4.7 32.6 1.0 CG A:ASP69 4.7 33.4 1.0 NE2 A:GLN11 4.8 24.4 1.0 OG1 A:THR145 4.8 23.8 1.0

Magnesium binding site 2 out of 4 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:24.2 occ:1.00 O B:HOH615 2.1 37.4 1.0 O1A B:GDP501 2.2 22.4 1.0 OE1 B:GLN11 2.3 41.4 1.0 O C:HOH667 2.4 27.0 1.0 O B:HOH639 2.4 34.7 1.0 O B:HOH635 3.1 37.0 1.0 OD2 B:ASP177 3.2 47.8 1.0 CD B:GLN11 3.4 40.6 1.0 PA B:GDP501 3.6 21.0 1.0 O3A B:GDP501 4.1 20.4 1.0 CG B:GLN11 4.1 36.8 1.0 CB B:GLN11 4.1 31.9 1.0 C5' B:GDP501 4.2 20.5 1.0 CG B:ASP177 4.3 36.6 1.0 ND2 B:ASN99 4.3 20.6 1.0 O5' B:GDP501 4.4 18.7 1.0 NE2 B:GLN11 4.5 43.3 1.0 O2A B:GDP501 4.7 20.2 1.0 O1B B:GDP501 4.7 21.6 1.0 C8 B:GDP501 4.8 22.5 1.0 OE1 C:GLU254 4.9 45.5 1.0 CB B:ASP177 5.0 34.4 1.0

Magnesium binding site 3 out of 4 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:22.9 occ:1.00 O1G C:GTP501 1.8 19.0 1.0 O C:HOH611 1.9 19.6 1.0 O1B C:GTP501 1.9 19.9 1.0 O C:HOH613 1.9 12.5 1.0 O C:HOH624 2.0 12.4 1.0 O C:HOH625 2.0 6.7 1.0 PG C:GTP501 2.9 19.6 1.0 PB C:GTP501 3.0 20.7 1.0 O3B C:GTP501 3.2 20.2 1.0 O2G C:GTP501 3.5 20.5 1.0 O3A C:GTP501 3.5 23.2 1.0 OD1 C:ASP69 4.1 19.1 1.0 OE2 C:GLU71 4.1 32.7 1.0 O3G C:GTP501 4.2 19.1 1.0 OD2 C:ASP69 4.2 20.7 1.0 OD2 C:ASP98 4.3 26.7 1.0 O2B C:GTP501 4.3 21.3 1.0 CB C:GLN11 4.3 23.0 1.0 CB C:ASP98 4.4 26.7 1.0 N C:GLN11 4.4 21.2 1.0 O1A C:GTP501 4.5 23.4 1.0 CG C:GLU71 4.6 28.8 1.0 CG C:ASP69 4.6 21.8 1.0 PA C:GTP501 4.6 23.3 1.0 CG C:ASP98 4.7 26.3 1.0 NE2 C:GLN11 4.8 24.0 1.0 NZ D:LYS252 4.8 48.4 1.0 OG1 C:THR145 4.8 22.4 1.0 CD C:GLU71 4.9 30.0 1.0 CA C:GLN11 4.9 22.3 1.0

Magnesium binding site 4 out of 4 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:68.2 occ:1.00 O3B D:GTP501 2.4 73.5 1.0 OE1 D:GLU69 2.5 0.8 1.0 O1G D:GTP501 3.0 86.9 1.0 PG D:GTP501 3.2 81.1 1.0 CD D:GLU69 3.4 0.9 1.0 O1B D:GTP501 3.4 52.8 1.0 O3G D:GTP501 3.5 79.2 1.0 PB D:GTP501 3.5 57.7 1.0 OE1 D:GLN11 3.6 66.4 1.0 CB D:GLN11 3.6 56.1 1.0 O3A D:GTP501 4.1 58.4 1.0 OE2 D:GLU69 4.1 97.5 1.0 CG D:GLU69 4.2 95.5 1.0 N D:GLN11 4.2 46.5 1.0 O1A D:GTP501 4.3 67.8 1.0 CD D:GLN11 4.4 62.9 1.0 CA D:GLN11 4.5 51.9 1.0 CG D:GLN11 4.5 59.6 1.0 OD1 D:ASP67 4.6 49.8 1.0 O2G D:GTP501 4.6 72.5 1.0 PA D:GTP501 4.6 54.3 1.0 CG2 D:THR72 4.6 0.7 1.0 OD2 D:ASP67 4.6 52.5 1.0 CG2 D:THR143 4.7 58.8 1.0 O2B D:GTP501 4.8 65.5 1.0 O2A D:GTP501 5.0 50.6 1.0

K.E.Arnst, S.Banerjee, Y.Wang, H.Chen, Y.Li, L.Yang, W.Li, D.D.Miller, W.Li. X-Ray Crystal Structure Guided Discovery and Antitumor Efficacy of Dihydroquinoxalinone As Potent Tubulin Polymerization Inhibitors. Acs Chem.Biol. 2019.
ISSN: ESSN 1554-8937
PubMed: 31714738
DOI: 10.1021/ACSCHEMBIO.9B00696