Magnesium in PDB 6o61: Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-231

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-231, PDB code: 6o61 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)	48.16 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.257, 157.092, 184.039, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.4

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-231 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 Abi-231 (pdb code 6o61). 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 Abi-231, PDB code: 6o61:
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 Abi-231


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 Abi-231 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:43.5 occ:1.00 O A:HOH611 1.9 33.5 1.0 O A:HOH641 2.0 25.0 1.0 O2G A:GTP501 2.0 38.9 1.0 O A:HOH636 2.1 36.3 1.0 O2B A:GTP501 2.2 29.3 1.0 O A:HOH603 2.2 29.7 1.0 PG A:GTP501 3.2 36.5 1.0 PB A:GTP501 3.2 34.6 1.0 O3B A:GTP501 3.6 40.2 1.0 O3A A:GTP501 3.7 31.3 1.0 O3G A:GTP501 4.0 37.2 1.0 CB A:GLN11 4.0 36.2 1.0 OD1 A:ASP69 4.3 32.9 1.0 O1G A:GTP501 4.4 27.6 1.0 OD2 A:ASP98 4.4 28.1 1.0 OD2 A:ASP69 4.4 35.0 1.0 CG A:GLU71 4.4 58.7 1.0 O2A A:GTP501 4.5 42.5 1.0 N A:GLN11 4.5 33.9 1.0 OE1 A:GLN11 4.5 36.2 1.0 CB A:ASP98 4.6 44.2 1.0 O1B A:GTP501 4.6 34.6 1.0 PA A:GTP501 4.6 31.4 1.0 OE1 A:GLU71 4.6 66.5 1.0 CG A:ASP98 4.7 39.4 1.0 CG A:ASP69 4.8 37.1 1.0 CA A:GLN11 4.8 37.0 1.0 NZ B:LYS252 4.9 53.9 1.0 CD A:GLN11 5.0 28.5 1.0 CD A:GLU71 5.0 62.7 1.0

Magnesium binding site 2 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-231


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 Abi-231 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:39.4 occ:1.00 OE1 B:GLN11 2.5 51.9 1.0 O C:HOH646 2.5 36.9 1.0 O2A B:GDP501 2.5 35.3 1.0 O B:HOH624 2.7 48.0 1.0 O B:HOH617 2.9 31.9 1.0 OD2 B:ASP177 3.6 59.4 1.0 CD B:GLN11 3.7 47.6 1.0 PA B:GDP501 3.7 36.0 1.0 O3A B:GDP501 3.9 42.2 1.0 ND2 B:ASN99 4.1 31.1 1.0 C5' B:GDP501 4.3 19.2 1.0 CG B:ASP177 4.5 55.9 1.0 O5' B:GDP501 4.5 19.8 1.0 CB B:GLN11 4.5 35.0 1.0 NE2 B:GLN11 4.5 46.5 1.0 OE1 C:GLU254 4.6 46.8 1.0 O C:HOH609 4.6 39.6 1.0 C8 B:GDP501 4.6 41.7 1.0 CG B:GLN11 4.7 38.8 1.0 O2B B:GDP501 4.9 26.3 1.0 OD1 B:ASN99 4.9 33.0 1.0 O1A B:GDP501 4.9 36.5 1.0 CB B:ASP177 4.9 51.4 1.0 CG B:ASN99 4.9 28.5 1.0

Magnesium binding site 3 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-231


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 Abi-231 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.5 occ:1.00 O C:HOH675 2.0 24.3 1.0 O C:HOH605 2.0 19.4 1.0 O3G C:GTP501 2.0 28.8 1.0 O2B C:GTP501 2.1 32.8 1.0 O C:HOH613 2.1 20.3 1.0 O C:HOH637 2.2 17.0 1.0 PG C:GTP501 3.2 29.6 1.0 PB C:GTP501 3.2 27.7 1.0 OE1 C:GLU71 3.5 51.3 1.0 O3B C:GTP501 3.7 33.6 1.0 O3A C:GTP501 3.7 27.7 1.0 O2G C:GTP501 3.8 28.8 1.0 CB C:GLN11 4.1 30.3 1.0 OD1 C:ASP69 4.3 29.2 1.0 OD2 C:ASP69 4.4 33.4 1.0 O1G C:GTP501 4.5 28.6 1.0 NZ D:LYS252 4.5 61.0 1.0 O2A C:GTP501 4.5 28.0 1.0 N C:GLN11 4.5 27.8 1.0 OE1 C:GLN11 4.5 30.0 1.0 O1B C:GTP501 4.5 27.2 1.0 OD2 C:ASP98 4.6 33.9 1.0 CB C:ASP98 4.6 30.1 1.0 PA C:GTP501 4.7 27.5 1.0 CD C:GLU71 4.7 49.7 1.0 CG C:ASP69 4.8 29.0 1.0 CG C:ASP98 4.9 36.9 1.0 CA C:GLN11 4.9 32.1 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