Magnesium in PDB 7lz7: Tubulin-RB3_SLD-Ttl in Complex with Compound 5K

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K, PDB code: 7lz7 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)	49.88 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.211, 157.998, 182.056, 90, 90, 90
R / Rfree (%)	17.1 / 21.1

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K 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 5K (pdb code 7lz7). 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 5K, PDB code: 7lz7:
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 5K


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 5K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:32.7 occ:1.00 O2G A:GTP501 2.0 23.5 1.0 O A:HOH609 2.1 32.5 1.0 O A:HOH604 2.1 30.9 1.0 O A:HOH601 2.1 37.1 1.0 O A:HOH620 2.2 35.3 1.0 O2B A:GTP501 2.2 15.8 1.0 PG A:GTP501 3.1 34.1 1.0 PB A:GTP501 3.2 27.7 1.0 O3B A:GTP501 3.5 40.8 1.0 O3A A:GTP501 3.5 36.4 1.0 O3G A:GTP501 3.6 30.2 1.0 OE2 A:GLU71 3.8 59.7 1.0 NZ B:LYS252 4.0 55.8 1.0 CB A:GLN11 4.1 30.9 1.0 OD1 A:ASP69 4.3 42.2 1.0 O2A A:GTP501 4.3 36.6 1.0 N A:GLN11 4.4 31.7 1.0 O1G A:GTP501 4.4 23.5 1.0 PA A:GTP501 4.5 34.0 1.0 OD2 A:ASP69 4.5 46.0 1.0 O1B A:GTP501 4.5 39.6 1.0 CB A:ASP98 4.6 35.7 1.0 OE1 A:GLN11 4.7 39.0 1.0 O A:HOH619 4.8 37.6 1.0 CA A:GLN11 4.8 35.3 1.0 CG A:ASP69 4.9 44.5 1.0 O1A A:GTP501 4.9 19.3 1.0

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


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 5K within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:22.4 occ:1.00 OE1 B:GLN11 2.1 53.1 1.0 O B:HOH603 2.2 29.0 1.0 O2A B:GDP502 2.2 25.6 1.0 O B:HOH601 2.2 57.1 1.0 O C:HOH638 2.2 49.0 1.0 O B:HOH628 2.3 32.2 1.0 CD B:GLN11 3.3 54.3 1.0 PA B:GDP502 3.4 25.9 1.0 O3A B:GDP502 3.6 36.3 1.0 OD2 B:ASP177 3.6 56.9 1.0 CB B:GLN11 4.1 34.5 1.0 ND2 B:ASN99 4.1 25.6 1.0 C5' B:GDP502 4.2 18.6 1.0 O5' B:GDP502 4.2 8.3 1.0 CG B:GLN11 4.2 46.0 1.0 NE2 B:GLN11 4.2 55.1 1.0 O1A B:GDP502 4.6 14.3 1.0 O2B B:GDP502 4.7 18.9 1.0 OE1 C:GLU254 4.7 54.6 1.0 CG B:ASP177 4.7 54.1 1.0 PB B:GDP502 4.8 25.1 1.0 C8 B:GDP502 5.0 31.6 1.0

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


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 5K within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:29.0 occ:1.00 O C:HOH606 1.9 36.5 1.0 O2B C:GTP501 2.0 23.0 1.0 O3G C:GTP501 2.1 18.9 1.0 O C:HOH609 2.1 16.7 1.0 O C:HOH603 2.1 26.6 1.0 O C:HOH649 2.2 43.3 1.0 PB C:GTP501 3.1 27.0 1.0 PG C:GTP501 3.3 23.7 1.0 OE1 C:GLU71 3.4 68.2 1.0 O3B C:GTP501 3.6 25.1 1.0 O3A C:GTP501 3.6 38.8 1.0 O2G C:GTP501 3.9 24.7 1.0 CB C:GLN11 4.1 22.6 1.0 OD1 C:ASP69 4.2 32.0 1.0 OD2 C:ASP69 4.3 31.9 1.0 NZ D:LYS252 4.4 64.1 1.0 N C:GLN11 4.4 22.0 1.0 O1B C:GTP501 4.4 25.4 1.0 O1G C:GTP501 4.5 18.7 1.0 O2A C:GTP501 4.5 31.1 1.0 PA C:GTP501 4.6 28.5 1.0 OD2 C:ASP98 4.6 53.6 1.0 CD C:GLU71 4.6 63.3 1.0 CB C:ASP98 4.7 29.0 1.0 CG C:ASP69 4.7 33.9 1.0 OE1 C:GLN11 4.8 36.0 1.0 CA C:GLN11 4.8 28.8 1.0 O1A C:GTP501 5.0 25.0 1.0

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


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 5K within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:62.4 occ:1.00 OE1 D:GLN11 2.2 110.0 1.0 O2A D:GTP501 2.2 68.2 1.0 O D:HOH601 3.2 45.9 1.0 CD D:GLN11 3.3 99.1 1.0 PA D:GTP501 3.5 51.9 1.0 O2G D:GTP501 3.5 107.8 1.0 O3A D:GTP501 3.7 62.6 1.0 NE2 D:GLN11 4.1 92.3 1.0 CB D:GLN11 4.2 83.6 1.0 OD1 D:ASN99 4.3 63.6 1.0 CG D:GLN11 4.4 94.8 1.0 O1A D:GTP501 4.5 43.4 1.0 C5' D:GTP501 4.5 42.4 1.0 O5' D:GTP501 4.5 50.1 1.0 O1B D:GTP501 4.6 51.6 1.0 PB D:GTP501 4.8 65.2 1.0 PG D:GTP501 4.9 106.4 1.0

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


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 5K within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:95.2 occ:1.00 O3G F:ACP402 2.0 110.1 1.0 OE1 F:GLU331 2.1 132.9 1.0 O2B F:ACP402 2.3 138.5 1.0 CD F:GLU331 3.1 119.8 1.0 PG F:ACP402 3.4 119.0 1.0 ND2 F:ASN333 3.4 92.1 1.0 OE2 F:GLU331 3.6 134.8 1.0 PB F:ACP402 3.7 131.3 1.0 NZ F:LYS74 3.8 77.4 1.0 O1G F:ACP402 3.8 119.0 1.0 CG F:ASN333 4.1 76.8 1.0 C3B F:ACP402 4.2 126.5 1.0 O1B F:ACP402 4.2 132.9 1.0 CG F:GLU331 4.4 91.6 1.0 O2G F:ACP402 4.5 114.1 1.0 CB F:ASN333 4.6 55.5 1.0 OD1 F:ASN333 4.8 75.6 1.0 O3A F:ACP402 5.0 120.0 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