Magnesium in PDB 6x1e: Tubulin-RB3_SLD-Ttl in Complex with Compound 5L

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5L, PDB code: 6x1e 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)	49.91 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.36, 157.742, 182.163, 90, 90, 90
R / Rfree (%)	17 / 22.4

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5L also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Magnesium atom in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5L (pdb code 6x1e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5L, PDB code: 6x1e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5L


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 5L within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:28.6 occ:1.00 O A:HOH603 2.0 33.8 1.0 O A:HOH604 2.0 42.5 1.0 O2G A:GTP501 2.1 19.7 1.0 O A:HOH602 2.1 55.1 1.0 O A:HOH616 2.2 45.9 1.0 O2B A:GTP501 2.3 29.9 1.0 PG A:GTP501 3.2 32.8 1.0 PB A:GTP501 3.3 44.8 1.0 OE2 A:GLU71 3.5 59.7 1.0 O3B A:GTP501 3.7 49.1 1.0 O3G A:GTP501 3.7 29.8 1.0 O3A A:GTP501 3.8 39.7 1.0 OD1 A:ASP69 4.2 45.1 1.0 CB A:GLN11 4.2 36.9 1.0 OD2 A:ASP69 4.3 53.8 1.0 NZ B:LYS252 4.5 63.3 1.0 N A:GLN11 4.5 38.7 1.0 O1G A:GTP501 4.5 23.5 1.0 CB A:ASP98 4.5 29.6 1.0 O1B A:GTP501 4.6 51.0 1.0 O2A A:GTP501 4.7 28.0 1.0 CG A:ASP69 4.7 51.8 1.0 CD A:GLU71 4.7 56.3 1.0 OE1 A:GLN11 4.8 34.9 1.0 PA A:GTP501 4.8 27.5 1.0 CG A:ASP98 4.9 49.1 1.0 CA A:GLN11 4.9 33.6 1.0

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


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 5L within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:51.1 occ:1.00 OE1 B:GLN11 2.0 72.1 1.0 O B:HOH605 2.1 53.8 1.0 O B:HOH601 2.1 96.9 1.0 O B:HOH622 2.2 58.5 1.0 O2A B:GDP501 2.3 25.3 1.0 O B:HOH625 2.5 40.3 1.0 CD B:GLN11 3.2 61.3 1.0 OD2 B:ASP177 3.4 75.7 1.0 PA B:GDP501 3.5 18.1 1.0 O3A B:GDP501 3.7 37.6 1.0 CB B:GLN11 4.1 49.0 1.0 ND2 B:ASN99 4.1 36.4 1.0 NE2 B:GLN11 4.1 58.5 1.0 CG B:GLN11 4.2 58.1 1.0 C5' B:GDP501 4.2 20.0 1.0 O5' B:GDP501 4.3 8.0 1.0 O1A B:GDP501 4.6 20.0 1.0 CG B:ASP177 4.6 70.0 1.0 O2B B:GDP501 4.6 29.5 1.0 PB B:GDP501 4.8 36.6 1.0 OE1 C:GLU254 4.9 58.6 1.0

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


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 5L within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:30.4 occ:1.00 O C:HOH611 2.0 45.8 1.0 O3G C:GTP501 2.0 25.1 1.0 O2B C:GTP501 2.1 33.5 1.0 O C:HOH629 2.2 55.5 1.0 O C:HOH602 2.2 21.4 1.0 O C:HOH601 2.2 22.4 1.0 PB C:GTP501 3.2 34.4 1.0 PG C:GTP501 3.3 55.0 1.0 OE1 C:GLU71 3.4 64.1 1.0 O3A C:GTP501 3.7 36.8 1.0 O3B C:GTP501 3.7 33.2 1.0 CB C:GLN11 4.1 22.7 1.0 O2G C:GTP501 4.2 26.8 1.0 OD2 C:ASP98 4.3 44.2 1.0 O1G C:GTP501 4.4 21.3 1.0 OD1 C:ASP69 4.4 32.7 1.0 OD2 C:ASP69 4.4 32.0 1.0 NZ D:LYS252 4.4 69.8 1.0 CD C:GLU71 4.5 58.1 1.0 N C:GLN11 4.5 21.9 1.0 OE1 C:GLN11 4.5 41.4 1.0 O2A C:GTP501 4.5 29.2 1.0 O1B C:GTP501 4.5 32.3 1.0 PA C:GTP501 4.6 42.9 1.0 CB C:ASP98 4.7 38.2 1.0 CG C:ASP69 4.9 35.4 1.0 CA C:GLN11 4.9 22.2 1.0 CG C:ASP98 5.0 42.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5L


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 5L within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:68.6 occ:1.00 OE1 D:GLN11 2.1 121.2 1.0 O2A D:GTP501 2.3 91.5 1.0 CD D:GLN11 3.3 107.9 1.0 O D:HOH601 3.5 51.2 1.0 PA D:GTP501 3.6 68.2 1.0 O2G D:GTP501 3.6 108.4 1.0 O3A D:GTP501 3.8 82.1 1.0 NE2 D:GLN11 4.1 100.8 1.0 OD1 D:ASN99 4.2 92.3 1.0 CB D:GLN11 4.3 97.9 1.0 CG D:GLN11 4.4 100.8 1.0 C5' D:GTP501 4.5 49.0 1.0 O5' D:GTP501 4.6 55.9 1.0 O1A D:GTP501 4.6 63.6 1.0 O1B D:GTP501 4.7 82.2 1.0 PB D:GTP501 4.9 88.1 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-RB3_SLD-Ttl in Complex with Compound 5L within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:97.4 occ:1.00 O3G F:ACP402 2.1 119.2 1.0 OE1 F:GLU331 2.1 131.0 1.0 O2B F:ACP402 2.2 131.4 1.0 CD F:GLU331 2.8 120.7 1.0 OE2 F:GLU331 2.9 135.6 1.0 ND2 F:ASN333 3.2 98.3 1.0 PG F:ACP402 3.4 124.8 1.0 PB F:ACP402 3.6 121.6 1.0 O1G F:ACP402 3.8 126.8 1.0 CG F:GLU331 4.1 102.2 1.0 C3B F:ACP402 4.2 117.6 1.0 CG F:ASN333 4.2 90.0 1.0 O1B F:ACP402 4.3 113.3 1.0 NZ F:LYS74 4.4 95.0 1.0 CE F:LYS74 4.5 83.8 1.0 O2G F:ACP402 4.5 110.2 1.0 OD1 F:ASN333 4.5 96.2 1.0 O3A F:ACP402 4.8 118.6 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