Magnesium in PDB 6d88: Tubulin-RB3_SLD-Ttl in Complex with Compound 13F

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 13F, PDB code: 6d88 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)	45.65 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.536, 157.894, 182.025, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.6

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 13F 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 13F (pdb code 6d88). 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 13F, PDB code: 6d88:
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 13F


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 13F within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:41.1 occ:1.00 O A:HOH601 1.9 42.0 1.0 O A:HOH604 2.0 45.2 1.0 O2B A:GTP501 2.6 29.7 1.0 O2G A:GTP501 2.7 37.3 1.0 OE2 A:GLU71 3.4 68.7 1.0 OD2 A:ASP69 3.6 51.1 1.0 PB A:GTP501 3.9 36.6 1.0 PG A:GTP501 3.9 45.6 1.0 OD1 A:ASP69 3.9 49.2 1.0 CB A:GLN11 4.0 42.2 1.0 CD A:GLU71 4.1 65.7 1.0 CG A:ASP69 4.2 50.1 1.0 OE1 A:GLN11 4.2 41.2 1.0 O3G A:GTP501 4.2 39.0 1.0 O3B A:GTP501 4.3 44.3 1.0 N A:GLN11 4.5 37.5 1.0 CB A:ASP98 4.5 45.6 1.0 OE1 A:GLU71 4.5 64.4 1.0 CB A:GLU71 4.7 60.1 1.0 CA A:GLN11 4.8 38.6 1.0 O3A A:GTP501 4.8 33.0 1.0 OD2 A:ASP98 4.8 51.6 1.0 CG2 A:VAL74 4.9 38.8 1.0 O1B A:GTP501 4.9 39.5 1.0 CD A:GLN11 4.9 39.1 1.0 O2A A:GTP501 5.0 38.5 1.0

Magnesium binding site 2 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 13F


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 13F within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:38.1 occ:1.00 O B:HOH619 2.4 43.8 1.0 O2A B:GDP501 2.4 27.0 1.0 OE1 B:GLN11 2.5 62.0 1.0 O C:HOH619 2.5 53.0 1.0 OD2 B:ASP177 2.9 68.6 1.0 O B:HOH608 3.5 29.2 1.0 CD B:GLN11 3.6 57.8 1.0 PA B:GDP501 3.7 26.2 1.0 C5' B:GDP501 4.0 19.8 1.0 O3A B:GDP501 4.1 35.1 1.0 CG B:ASP177 4.1 66.2 1.0 ND2 B:ASN99 4.3 26.0 1.0 O5' B:GDP501 4.3 19.9 1.0 NE2 B:GLN11 4.3 58.4 1.0 CB B:GLN11 4.5 43.2 1.0 CG B:GLN11 4.6 50.2 1.0 CB B:ASP177 4.7 58.4 1.0 OE2 C:GLU254 4.7 61.4 1.0 C8 B:GDP501 4.8 34.1 1.0 O1A B:GDP501 4.9 33.9 1.0 OE1 C:GLU254 5.0 63.3 1.0 O2B B:GDP501 5.0 36.5 1.0

Magnesium binding site 3 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 13F


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 13F within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:41.9 occ:1.00 O C:HOH601 1.9 34.4 1.0 O3G C:GTP501 2.1 43.0 1.0 O C:HOH602 2.2 32.3 1.0 O2B C:GTP501 2.6 33.6 1.0 PG C:GTP501 3.4 34.7 1.0 OE1 C:GLU71 3.5 51.8 1.0 O2G C:GTP501 3.7 31.4 1.0 CG C:GLU71 3.8 40.8 1.0 PB C:GTP501 3.8 32.9 1.0 CB C:ASP98 3.9 33.5 1.0 OD2 C:ASP98 3.9 48.7 1.0 O3B C:GTP501 4.0 33.1 1.0 CD C:GLU71 4.1 47.9 1.0 CG C:ASP98 4.2 41.9 1.0 OD1 C:ASP69 4.2 40.1 1.0 OD2 C:ASP69 4.3 40.1 1.0 O3A C:GTP501 4.4 32.4 1.0 NZ D:LYS252 4.5 60.4 1.0 O1G C:GTP501 4.6 28.7 1.0 CG C:ASP69 4.7 38.0 1.0 CB C:GLN11 4.7 28.8 1.0 OD1 D:ASN247 4.9 0.6 1.0 OE1 C:GLN11 5.0 46.1 1.0

Q.Wang, K.E.Arnst, Y.Wang, G.Kumar, D.Ma, H.Chen, Z.Wu, J.Yang, S.W.White, D.D.Miller, W.Li. Structural Modification of the 3,4,5-Trimethoxyphenyl Moiety in the Tubulin Inhibitor Veru-111 Leads to Improved Antiproliferative Activities. J. Med. Chem. V. 61 7877 2018.
ISSN: ISSN 1520-4804
PubMed: 30122035
DOI: 10.1021/ACS.JMEDCHEM.8B00827