Magnesium in PDB 6pc4: Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-274

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-274, PDB code: 6pc4 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)	41.74 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.143, 157.533, 181.961, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.4

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-274 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-274 (pdb code 6pc4). 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-274, PDB code: 6pc4:
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-274


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-274 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:24.7 occ:1.00 O A:HOH629 2.1 25.1 1.0 O2G A:GTP501 2.1 23.8 1.0 O A:HOH662 2.1 24.1 1.0 O A:HOH603 2.2 39.8 1.0 O A:HOH601 2.3 37.5 1.0 O2B A:GTP501 2.3 27.3 1.0 PG A:GTP501 3.4 29.4 1.0 PB A:GTP501 3.4 24.4 1.0 OE2 A:GLU71 3.5 43.6 1.0 O3B A:GTP501 3.8 39.0 1.0 O3A A:GTP501 3.8 32.0 1.0 O3G A:GTP501 3.9 31.9 1.0 CB A:GLN11 4.1 31.4 1.0 OD2 A:ASP98 4.1 41.7 1.0 OD1 A:ASP69 4.3 44.4 1.0 OD2 A:ASP69 4.3 43.0 1.0 OE1 A:GLN11 4.4 35.2 1.0 CB A:ASP98 4.5 37.6 1.0 N A:GLN11 4.6 32.4 1.0 O1G A:GTP501 4.6 23.4 1.0 O2A A:GTP501 4.7 30.5 1.0 CD A:GLU71 4.7 45.6 1.0 CG A:ASP98 4.7 38.9 1.0 O1B A:GTP501 4.7 38.7 1.0 CG A:ASP69 4.8 44.5 1.0 NZ B:LYS252 4.8 52.5 1.0 PA A:GTP501 4.8 28.3 1.0 CA A:GLN11 4.9 33.1 1.0 CD A:GLN11 5.0 30.9 1.0

Magnesium binding site 2 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-274


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-274 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:35.6 occ:1.00 O B:HOH615 2.0 32.5 1.0 OE1 B:GLN11 2.1 37.4 1.0 O2A B:GDP501 2.2 30.0 1.0 O B:HOH605 2.2 45.4 1.0 O C:HOH645 2.3 31.6 1.0 O B:HOH657 2.3 37.2 1.0 CD B:GLN11 3.3 40.0 1.0 PA B:GDP501 3.5 24.7 1.0 OD2 B:ASP177 3.6 43.6 1.0 O3A B:GDP501 3.8 22.4 1.0 CB B:GLN11 4.0 33.0 1.0 C5' B:GDP501 4.2 18.1 1.0 NE2 B:GLN11 4.2 45.6 1.0 CG B:GLN11 4.2 36.0 1.0 O5' B:GDP501 4.3 22.3 1.0 OD1 B:ASN99 4.3 30.9 1.0 O2B B:GDP501 4.5 21.8 1.0 O1A B:GDP501 4.6 23.6 1.0 OE1 C:GLU254 4.6 40.8 1.0 CG B:ASP177 4.7 42.6 1.0 C8 B:GDP501 4.7 29.1 1.0 PB B:GDP501 4.8 27.7 1.0

Magnesium binding site 3 out of 3 in the Tubulin-RB3_SLD-Ttl in Complex with Compound Abi-274


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-274 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:26.0 occ:1.00 O C:HOH631 2.0 25.1 1.0 O3G C:GTP501 2.0 24.9 1.0 O C:HOH640 2.0 28.6 1.0 O C:HOH610 2.1 25.4 1.0 O2B C:GTP501 2.1 27.3 1.0 O C:HOH624 2.1 29.5 1.0 PG C:GTP501 3.2 27.7 1.0 PB C:GTP501 3.2 24.1 1.0 O3B C:GTP501 3.5 30.7 1.0 O3A C:GTP501 3.7 26.3 1.0 O2G C:GTP501 3.7 25.5 1.0 OE1 C:GLU71 3.8 39.5 1.0 OD1 C:ASP69 4.0 27.6 1.0 OD2 C:ASP69 4.1 25.4 1.0 CB C:GLN11 4.2 24.7 1.0 NZ D:LYS252 4.3 54.6 1.0 OD2 C:ASP98 4.3 40.1 1.0 O1G C:GTP501 4.4 26.9 1.0 N C:GLN11 4.4 24.2 1.0 CB C:ASP98 4.5 35.8 1.0 O1B C:GTP501 4.5 23.8 1.0 CG C:ASP69 4.5 29.9 1.0 OE1 C:GLN11 4.7 38.1 1.0 O2A C:GTP501 4.8 29.4 1.0 CG C:ASP98 4.8 39.4 1.0 PA C:GTP501 4.8 23.9 1.0 ND2 D:ASN247 4.8 0.1 1.0 CA C:GLN11 4.9 27.5 1.0 OG1 C:THR145 4.9 27.0 1.0 CD C:GLU71 5.0 39.0 1.0

H.Chen, S.Deng, Y.Wang, N.Albadari, G.Kumar, D.Ma, W.Li, S.W.White, D.D.Miller, W.Li. Structure-Activity Relationship Study of Novel 6-Aryl-2-Benzoyl-Pyridines As Tubulin Polymerization Inhibitors with Potent Antiproliferative Properties. J.Med.Chem. V. 63 827 2020.
ISSN: ISSN 0022-2623
PubMed: 31860298
DOI: 10.1021/ACS.JMEDCHEM.9B01815