Magnesium in PDB 6x1f: Tubulin-RB3_SLD-Ttl in Complex with Compound 5M

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5M, PDB code: 6x1f was solved by S.W.White, M.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.24 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.48, 157.923, 182.205, 90, 90, 90
R / Rfree (%)	19 / 24.1

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5M 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 5M (pdb code 6x1f). 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 5M, PDB code: 6x1f:
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 5M


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 5M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:24.3 occ:1.00 O A:HOH606 2.1 26.9 1.0 O2G A:GTP501 2.1 20.8 1.0 O A:HOH603 2.1 34.0 1.0 O2B A:GTP501 2.1 17.2 1.0 O A:HOH647 2.2 28.2 1.0 O A:HOH608 2.2 29.7 1.0 PG A:GTP501 3.2 24.5 1.0 PB A:GTP501 3.3 22.6 1.0 OE2 A:GLU71 3.6 45.1 1.0 O3G A:GTP501 3.6 21.2 1.0 O3B A:GTP501 3.6 33.9 1.0 O3A A:GTP501 3.7 29.1 1.0 OD1 A:ASP69 4.1 36.4 1.0 CB A:GLN11 4.2 31.3 1.0 N A:GLN11 4.4 30.1 1.0 OD2 A:ASP69 4.4 37.9 1.0 O1G A:GTP501 4.5 16.9 1.0 O1B A:GTP501 4.6 37.0 1.0 CB A:ASP98 4.6 32.0 1.0 NZ B:LYS252 4.6 46.6 1.0 O2A A:GTP501 4.7 31.1 1.0 CG A:ASP69 4.7 38.1 1.0 PA A:GTP501 4.7 28.3 1.0 OE1 A:GLN11 4.8 31.6 1.0 CD A:GLU71 4.8 44.1 1.0 CA A:GLN11 4.9 29.6 1.0 OD2 A:ASP98 4.9 39.0 1.0 CG A:ASP98 4.9 36.9 1.0

Magnesium binding site 2 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5M


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 5M within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:41.2 occ:1.00 OE1 B:GLN11 2.1 65.7 1.0 O B:HOH621 2.1 45.7 1.0 O B:HOH604 2.2 47.5 1.0 O C:HOH677 2.3 47.5 1.0 O B:HOH649 2.3 42.2 1.0 O2A B:GDP501 2.4 21.0 1.0 CD B:GLN11 3.3 59.7 1.0 PA B:GDP501 3.7 22.9 1.0 O3A B:GDP501 3.9 26.5 1.0 OD2 B:ASP177 4.0 64.1 1.0 CB B:GLN11 4.1 42.1 1.0 NE2 B:GLN11 4.2 58.9 1.0 ND2 B:ASN99 4.2 24.1 1.0 CG B:GLN11 4.3 51.4 1.0 O2B B:GDP501 4.4 23.5 1.0 C5' B:GDP501 4.4 20.6 1.0 O5' B:GDP501 4.5 16.6 1.0 O1A B:GDP501 4.8 21.3 1.0 OE1 C:GLU254 4.8 45.4 1.0 PB B:GDP501 4.9 18.9 1.0 CG B:ASP177 4.9 59.6 1.0

Magnesium binding site 3 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5M


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 5M within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:14.7 occ:1.00 O C:HOH604 2.0 27.1 1.0 O C:HOH602 2.1 25.8 1.0 O3G C:GTP501 2.1 19.2 1.0 O2B C:GTP501 2.1 23.9 1.0 O C:HOH601 2.2 18.1 1.0 O C:HOH687 2.2 36.3 1.0 PB C:GTP501 3.3 21.5 1.0 PG C:GTP501 3.4 21.6 1.0 OE1 C:GLU71 3.4 39.4 1.0 O3A C:GTP501 3.7 24.5 1.0 O3B C:GTP501 3.8 23.3 1.0 CB C:GLN11 4.1 21.6 1.0 O2G C:GTP501 4.1 22.0 1.0 OD1 C:ASP69 4.2 25.8 1.0 OD2 C:ASP69 4.3 29.6 1.0 OD2 C:ASP98 4.3 33.2 1.0 N C:GLN11 4.5 20.7 1.0 O1G C:GTP501 4.5 23.2 1.0 O1B C:GTP501 4.6 18.1 1.0 OE1 C:GLN11 4.6 36.2 1.0 O C:HOH685 4.6 43.5 1.0 O2A C:GTP501 4.6 21.4 1.0 NZ D:LYS252 4.6 44.2 1.0 CB C:ASP98 4.6 29.9 1.0 CD C:GLU71 4.6 40.0 1.0 PA C:GTP501 4.7 25.2 1.0 CG C:ASP69 4.7 28.7 1.0 CA C:GLN11 4.9 31.2 1.0 CG C:ASP98 4.9 34.3 1.0

S.Banerjee, F.Mahmud, S.Deng, L.Ma, M.K.Yun, S.O.Fakayode, K.E.Arnst, L.Yang, H.Chen, Z.Wu, P.B.Lukka, K.Parmar, B.Meibohm, S.W.White, Y.Wang, W.Li, D.D.Miller. X-Ray Crystallography-Guided Design, Antitumor Efficacy, and Qsar Analysis of Metabolically Stable Cyclopenta-Pyrimidinyl Dihydroquinoxalinone As A Potent Tubulin Polymerization Inhibitor. J.Med.Chem. V. 64 13072 2021.
ISSN: ISSN 0022-2623
PubMed: 34406768
DOI: 10.1021/ACS.JMEDCHEM.1C01202