Magnesium in PDB 6x1c: Tubulin-RB3_SLD-Ttl in Complex with Compound 5J

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5J, PDB code: 6x1c 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)	48.14 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.345, 158.32, 181.949, 90, 90, 90
R / Rfree (%)	17.4 / 21.6

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5J 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 5J (pdb code 6x1c). 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 5J, PDB code: 6x1c:
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 5J


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 5J within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:32.4 occ:1.00 O A:HOH602 2.0 25.5 1.0 O2B A:GTP501 2.1 18.5 1.0 O2G A:GTP501 2.1 17.3 1.0 O A:HOH604 2.1 34.9 1.0 O A:HOH611 2.2 46.0 1.0 O A:HOH612 2.2 42.1 1.0 PG A:GTP501 3.3 32.6 1.0 PB A:GTP501 3.3 36.9 1.0 O3G A:GTP501 3.7 25.2 1.0 OE2 A:GLU71 3.7 39.1 1.0 O3B A:GTP501 3.7 38.9 1.0 O3A A:GTP501 3.7 35.2 1.0 CB A:GLN11 4.1 31.7 1.0 O2A A:GTP501 4.4 25.7 1.0 OD1 A:ASP69 4.4 37.4 1.0 OD2 A:ASP98 4.4 48.5 1.0 N A:GLN11 4.4 25.4 1.0 OD2 A:ASP69 4.5 46.2 1.0 O1G A:GTP501 4.5 21.8 1.0 NZ B:LYS252 4.5 59.3 1.0 OE1 A:GLN11 4.5 33.0 1.0 O1B A:GTP501 4.6 36.5 1.0 PA A:GTP501 4.6 20.2 1.0 CB A:ASP98 4.7 32.8 1.0 CA A:GLN11 4.9 27.6 1.0 CG A:ASP69 4.9 46.9 1.0 CG A:ASP98 4.9 43.7 1.0 CD A:GLU71 4.9 45.4 1.0

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


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 5J within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:37.5 occ:1.00 OE1 B:GLN11 2.1 60.7 1.0 O2A B:GDP501 2.1 20.7 1.0 O C:HOH623 2.1 42.3 1.0 O B:HOH607 2.1 41.5 1.0 O B:HOH601 2.2 46.7 1.0 O B:HOH622 2.3 36.2 1.0 CD B:GLN11 3.3 48.0 1.0 PA B:GDP501 3.6 30.9 1.0 OD2 B:ASP177 3.7 62.0 1.0 O3A B:GDP501 4.1 32.4 1.0 CB B:GLN11 4.1 29.2 1.0 ND2 B:ASN99 4.1 28.7 1.0 NE2 B:GLN11 4.2 45.3 1.0 CG B:GLN11 4.3 41.8 1.0 C5' B:GDP501 4.3 12.4 1.0 O2B B:GDP501 4.4 24.6 1.0 O5' B:GDP501 4.4 11.9 1.0 O1A B:GDP501 4.5 11.6 1.0 PB B:GDP501 4.8 27.0 1.0 CG B:ASP177 4.8 59.3 1.0 OE1 C:GLU254 4.9 55.6 1.0

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


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 5J within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:32.2 occ:1.00 O3G C:GTP501 2.0 19.6 1.0 O C:HOH607 2.1 46.6 1.0 O C:HOH603 2.1 21.1 1.0 O2B C:GTP501 2.1 26.4 1.0 O C:HOH629 2.2 61.7 1.0 O C:HOH601 2.2 20.7 1.0 PB C:GTP501 3.3 28.0 1.0 PG C:GTP501 3.4 36.9 1.0 OE1 C:GLU71 3.5 68.1 1.0 O3B C:GTP501 3.8 22.2 1.0 O3A C:GTP501 3.8 34.5 1.0 CB C:GLN11 4.0 21.8 1.0 O2G C:GTP501 4.3 27.5 1.0 O1G C:GTP501 4.3 18.9 1.0 OE1 C:GLN11 4.4 37.1 1.0 OD2 C:ASP98 4.4 48.5 1.0 NZ D:LYS252 4.4 56.5 1.0 OD1 C:ASP69 4.4 30.3 1.0 N C:GLN11 4.5 21.1 1.0 OD2 C:ASP69 4.5 27.4 1.0 CD C:GLU71 4.5 61.0 1.0 O2A C:GTP501 4.5 26.8 1.0 O1B C:GTP501 4.6 20.8 1.0 PA C:GTP501 4.7 30.4 1.0 CB C:ASP98 4.7 34.6 1.0 ND2 D:ASN247 4.8 119.7 1.0 CA C:GLN11 4.9 21.4 1.0 CG C:ASP69 4.9 34.0 1.0 O1A C:GTP501 5.0 19.7 1.0

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


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 5J within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:61.9 occ:1.00 OE1 D:GLN11 2.1 114.6 1.0 O2A D:GTP501 2.3 79.2 1.0 O D:HOH601 3.1 49.9 1.0 CD D:GLN11 3.3 93.0 1.0 O2G D:GTP501 3.4 109.1 1.0 PA D:GTP501 3.7 61.7 1.0 O3A D:GTP501 3.9 68.8 1.0 NE2 D:GLN11 4.1 87.0 1.0 CB D:GLN11 4.3 83.0 1.0 CG D:GLN11 4.4 88.6 1.0 OD1 D:ASN99 4.5 74.4 1.0 C5' D:GTP501 4.6 44.9 1.0 O5' D:GTP501 4.6 59.0 1.0 O1A D:GTP501 4.6 60.4 1.0 O1B D:GTP501 4.8 54.2 1.0 PG D:GTP501 4.9 107.2 1.0 PB D:GTP501 5.0 67.7 1.0

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


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 5J within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:101.9 occ:1.00 O3G F:ACP401 2.0 116.6 1.0 OE1 F:GLU331 2.1 137.1 1.0 O2B F:ACP401 2.2 121.2 1.0 CD F:GLU331 3.0 125.0 1.0 ND2 F:ASN333 3.1 91.7 1.0 PG F:ACP401 3.2 116.5 1.0 OE2 F:GLU331 3.3 139.7 1.0 NZ F:LYS74 3.5 74.7 1.0 PB F:ACP401 3.6 113.4 1.0 O1G F:ACP401 3.6 119.1 1.0 C3B F:ACP401 4.1 110.9 1.0 O1B F:ACP401 4.2 110.1 1.0 CG F:ASN333 4.2 83.9 1.0 CG F:GLU331 4.3 99.7 1.0 O2G F:ACP401 4.4 105.3 1.0 CE F:LYS74 4.8 82.8 1.0 OD1 F:ASN333 4.8 87.7 1.0 O3A F:ACP401 4.8 105.2 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