Magnesium in PDB 6o5n: Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB, PDB code: 6o5n 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)	41.78 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.301, 157.764, 182.084, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.5

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB 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 10AB (pdb code 6o5n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB, PDB code: 6o5n:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB


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 10AB within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.9 occ:1.00 O2B A:GTP501 2.2 39.2 1.0 O2G A:GTP501 2.4 33.1 1.0 OE2 A:GLU71 2.9 70.5 1.0 PB A:GTP501 3.5 38.9 1.0 OD2 A:ASP69 3.5 49.0 1.0 PG A:GTP501 3.6 35.9 1.0 OD1 A:ASP69 3.7 50.9 1.0 O3B A:GTP501 3.9 39.9 1.0 CG A:ASP69 4.0 50.3 1.0 CD A:GLU71 4.1 69.5 1.0 O3G A:GTP501 4.1 37.8 1.0 CB A:GLN11 4.2 41.3 1.0 CB A:ASP98 4.3 56.5 1.0 N A:GLN11 4.3 40.1 1.0 O1B A:GTP501 4.5 39.8 1.0 OD2 A:ASP98 4.5 54.1 1.0 O3A A:GTP501 4.5 42.0 1.0 OD1 B:ASN247 4.6 0.8 1.0 OE1 A:GLU71 4.7 72.1 1.0 CG A:ASP98 4.8 54.7 1.0 CB A:GLU71 4.8 61.9 1.0 CA A:GLN11 4.8 39.7 1.0 O1G A:GTP501 4.8 30.1 1.0

Magnesium binding site 2 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB


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 10AB within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:24.1 occ:1.00 O B:HOH603 2.0 26.8 1.0 O2A B:GDP501 2.4 31.8 1.0 OE1 B:GLN11 2.4 40.8 1.0 OD2 B:ASP177 2.6 41.7 1.0 CD B:GLN11 3.5 40.6 1.0 PA B:GDP501 3.7 31.6 1.0 CG B:ASP177 3.8 42.6 1.0 C5' B:GDP501 3.9 22.2 1.0 NE2 B:GLN11 4.2 42.9 1.0 O3A B:GDP501 4.2 34.5 1.0 ND2 B:ASN99 4.3 42.1 1.0 O5' B:GDP501 4.3 21.0 1.0 OE2 C:GLU254 4.5 47.0 1.0 CB B:ASP177 4.6 41.2 1.0 CB B:GLN11 4.6 37.2 1.0 CG B:GLN11 4.7 38.9 1.0 OD1 B:ASP177 4.7 42.9 1.0 OE1 C:GLU254 4.7 48.6 1.0 C8 B:GDP501 4.8 32.6 1.0 O1A B:GDP501 4.8 26.8 1.0 CD C:GLU254 4.9 46.5 1.0 OD1 B:ASN99 4.9 44.9 1.0

Magnesium binding site 3 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 10AB


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 10AB within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:28.9 occ:1.00 O2B C:GTP501 2.3 44.9 1.0 O3G C:GTP501 2.5 46.3 1.0 OE1 C:GLU71 2.8 51.1 1.0 OD2 C:ASP69 3.4 35.8 1.0 PB C:GTP501 3.6 40.9 1.0 OD1 C:ASP69 3.7 37.5 1.0 PG C:GTP501 3.8 45.2 1.0 CD C:GLU71 3.9 49.8 1.0 CG C:ASP69 4.0 36.7 1.0 O3B C:GTP501 4.1 44.2 1.0 CB C:GLN11 4.1 29.6 1.0 N C:GLN11 4.4 27.5 1.0 OD2 C:ASP98 4.4 43.1 1.0 CB C:ASP98 4.5 39.8 1.0 O2G C:GTP501 4.6 45.1 1.0 OE2 C:GLU71 4.6 52.8 1.0 O3A C:GTP501 4.6 45.4 1.0 O1B C:GTP501 4.6 37.8 1.0 CB C:GLU71 4.7 41.0 1.0 CG2 C:VAL74 4.7 40.2 1.0 CA C:GLN11 4.8 28.9 1.0 ND2 D:ASN247 4.8 1.0 1.0 O1G C:GTP501 4.8 41.9 1.0 CG C:ASP98 4.9 41.6 1.0 OE1 C:GLN11 4.9 39.6 1.0 CG C:GLU71 4.9 44.4 1.0

Q.Wang, K.E.Arnst, Y.Wang, G.Kumar, D.Ma, S.W.White, D.D.Miller, W.Li, W.Li. Structure-Guided Design, Synthesis, and Biological Evaluation of (2-(1H-Indol-3-Yl)-1H-Imidazol-4-Yl)(3,4,5-Trimethoxyphenyl) Methanone (Abi-231) Analogues Targeting the Colchicine Binding Site in Tubulin. J.Med.Chem. V. 62 6734 2019.
ISSN: ISSN 0022-2623
PubMed: 31251599
DOI: 10.1021/ACS.JMEDCHEM.9B00706