Magnesium in PDB 6o5m: Tubulin-RB3_SLD-Ttl in Complex with Compound 10BB

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 10BB, PDB code: 6o5m 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)	49.76 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.966, 157.721, 181.615, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.3

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 10BB 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 10BB (pdb code 6o5m). 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 10BB, PDB code: 6o5m:
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 10BB


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 10BB within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:27.0 occ:1.00 O A:HOH669 2.0 31.1 1.0 O2G A:GTP501 2.0 25.5 1.0 O A:HOH712 2.1 27.5 1.0 O A:HOH667 2.1 29.9 1.0 O A:HOH608 2.1 23.4 1.0 O2B A:GTP501 2.2 23.3 1.0 PG A:GTP501 3.2 34.0 1.0 PB A:GTP501 3.3 23.6 1.0 O3G A:GTP501 3.6 28.4 1.0 O A:HOH633 3.7 39.1 1.0 O3B A:GTP501 3.7 38.2 1.0 O3A A:GTP501 3.9 22.1 1.0 OE2 A:GLU71 4.0 47.0 1.0 OD1 A:ASP69 4.1 32.3 1.0 OD2 A:ASP69 4.1 33.1 1.0 CB A:GLN11 4.1 25.7 1.0 CG A:GLU71 4.2 51.6 1.0 CB A:ASP98 4.3 27.4 1.0 OD2 A:ASP98 4.3 36.4 1.0 O1G A:GTP501 4.5 24.4 1.0 N A:GLN11 4.5 25.8 1.0 OE1 A:GLN11 4.5 32.3 1.0 CG A:ASP69 4.5 34.3 1.0 CD A:GLU71 4.6 51.1 1.0 O1B A:GTP501 4.6 35.4 1.0 CG A:ASP98 4.7 35.4 1.0 O2A A:GTP501 4.8 26.2 1.0 CA A:GLN11 4.9 26.0 1.0 PA A:GTP501 4.9 22.0 1.0

Magnesium binding site 2 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 10BB


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 10BB within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:41.6 occ:1.00 O B:HOH607 2.3 42.3 1.0 O2A B:GDP501 2.4 24.9 1.0 O B:HOH687 3.1 38.4 1.0 OE1 B:GLN11 3.4 47.3 1.0 OD2 B:ASP177 3.4 66.1 1.0 PA B:GDP501 3.6 21.4 1.0 O3A B:GDP501 3.8 18.8 1.0 CD B:GLN11 4.0 41.5 1.0 C5' B:GDP501 4.0 21.6 1.0 OD1 B:ASN99 4.2 25.3 1.0 O5' B:GDP501 4.2 20.2 1.0 O B:HOH694 4.2 43.1 1.0 NE2 B:GLN11 4.4 43.1 1.0 CG B:ASP177 4.5 63.2 1.0 O C:HOH640 4.6 43.3 1.0 CB B:GLN11 4.7 20.5 1.0 O1A B:GDP501 4.8 19.0 1.0 CB B:ASP177 4.9 58.3 1.0 C8 B:GDP501 4.9 25.1 1.0 CG B:GLN11 5.0 27.0 1.0

Magnesium binding site 3 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 10BB


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 10BB within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:23.7 occ:1.00 O3G C:GTP501 2.0 21.1 1.0 O C:HOH620 2.0 21.6 1.0 O C:HOH645 2.1 21.4 1.0 O2B C:GTP501 2.1 20.6 1.0 O C:HOH770 2.1 22.4 1.0 O C:HOH648 2.1 23.2 1.0 PB C:GTP501 3.2 20.3 1.0 PG C:GTP501 3.2 28.1 1.0 O3B C:GTP501 3.6 25.3 1.0 O3A C:GTP501 3.7 21.0 1.0 O2G C:GTP501 3.8 32.9 1.0 OE2 C:GLU71 4.0 36.5 1.0 OD1 C:ASP69 4.0 21.6 1.0 CB C:GLN11 4.1 20.8 1.0 OD2 C:ASP69 4.1 23.7 1.0 NZ D:LYS252 4.3 47.6 1.0 CG C:GLU71 4.3 31.5 1.0 N C:GLN11 4.3 20.5 1.0 OD2 C:ASP98 4.4 35.3 1.0 O1G C:GTP501 4.5 27.0 1.0 CB C:ASP98 4.5 22.3 1.0 O1B C:GTP501 4.5 19.9 1.0 CG C:ASP69 4.5 24.2 1.0 O2A C:GTP501 4.6 22.1 1.0 CD C:GLU71 4.6 33.3 1.0 OE1 C:GLN11 4.7 34.8 1.0 PA C:GTP501 4.7 20.6 1.0 CA C:GLN11 4.8 20.7 1.0 CG C:ASP98 4.8 30.2 1.0

Magnesium binding site 4 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 10BB


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 10BB within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:81.1 occ:1.00 O1B F:ACP402 2.2 88.5 1.0 OE1 F:GLU331 2.5 85.1 1.0 O1G F:ACP402 2.8 0.6 1.0 OE2 F:GLU331 2.8 86.5 1.0 CD F:GLU331 3.0 82.1 1.0 ND2 F:ASN333 3.4 86.0 1.0 PB F:ACP402 3.5 95.1 1.0 NZ F:LYS74 3.6 54.0 1.0 PG F:ACP402 4.0 0.7 1.0 C3B F:ACP402 4.1 0.4 1.0 O2B F:ACP402 4.2 96.7 1.0 CG F:GLU331 4.5 72.5 1.0 CG F:ASN333 4.6 78.3 1.0 O3A F:ACP402 4.7 89.9 1.0 O2G F:ACP402 4.9 0.6 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