Magnesium in PDB 7au5: Tubulin-Noscapine-Analogue-14E Complex

The structure of Tubulin-Noscapine-Analogue-14E Complex, PDB code: 7au5 was solved by C.Yong, S.M.Devine, A.-C.Abel, D.Muthiah, X.Gao, R.Callaghan, B.Capuano, M.O.Steinmetz, A.E.Prota, P.J.Scammels, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.88 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.642, 157.838, 180.35, 90, 90, 90
R / Rfree (%)	17.8 / 21.2

The structure of Tubulin-Noscapine-Analogue-14E Complex also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Magnesium atom in the Tubulin-Noscapine-Analogue-14E Complex (pdb code 7au5). 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-Noscapine-Analogue-14E Complex, PDB code: 7au5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Noscapine-Analogue-14E Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Noscapine-Analogue-14E Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:47.7 occ:1.00 O1G A:GTP501 2.0 40.3 1.0 O A:HOH617 2.0 49.6 1.0 O A:HOH651 2.1 50.1 1.0 O1B A:GTP501 2.1 42.7 1.0 O A:HOH601 2.2 51.0 1.0 O A:HOH657 2.2 47.1 1.0 PG A:GTP501 3.2 50.5 1.0 PB A:GTP501 3.3 46.2 1.0 O3B A:GTP501 3.5 64.3 1.0 O2G A:GTP501 3.7 49.2 1.0 OE2 A:GLU71 3.7 73.2 1.0 O3A A:GTP501 3.8 54.5 1.0 NZ B:LYS254 3.8 58.0 1.0 OD1 A:ASP69 4.1 54.4 1.0 CB A:GLN11 4.2 44.6 1.0 CG A:GLU71 4.2 70.0 1.0 OD2 A:ASP69 4.2 53.5 1.0 OD2 A:ASP98 4.2 58.6 1.0 NE2 A:GLN11 4.3 62.1 1.0 CB A:ASP98 4.4 56.1 1.0 CD A:GLU71 4.4 70.9 1.0 O3G A:GTP501 4.4 47.3 1.0 N A:GLN11 4.5 52.6 1.0 O2B A:GTP501 4.5 51.5 1.0 CG A:ASP69 4.6 58.1 1.0 O1A A:GTP501 4.6 51.4 1.0 CG A:ASP98 4.7 55.4 1.0 PA A:GTP501 4.8 50.9 1.0 CA A:GLN11 4.9 50.5 1.0 CE B:LYS254 5.0 59.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Noscapine-Analogue-14E Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Noscapine-Analogue-14E Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:35.7 occ:1.00 O B:HOH661 2.0 41.6 1.0 OE1 B:GLN11 2.2 47.9 1.0 O1A B:GDP501 2.3 41.3 1.0 O C:HOH676 2.3 49.3 1.0 O B:HOH680 2.6 49.3 1.0 O B:HOH625 2.7 53.0 1.0 O B:HOH737 3.0 58.4 1.0 CD B:GLN11 3.4 57.8 1.0 PA B:GDP501 3.6 39.0 1.0 O3A B:GDP501 3.9 45.4 1.0 OD2 B:ASP179 4.0 48.0 1.0 CB B:GLN11 4.1 41.4 1.0 CG B:GLN11 4.2 53.3 1.0 OD1 B:ASN101 4.4 45.3 1.0 NE2 B:GLN11 4.4 49.6 1.0 C5' B:GDP501 4.5 43.2 1.0 O5' B:GDP501 4.5 42.3 1.0 O1B B:GDP501 4.5 37.8 1.0 O2A B:GDP501 4.6 39.7 1.0 O C:HOH611 4.6 59.2 1.0 OE1 C:GLU254 4.7 53.1 1.0 PB B:GDP501 4.8 39.5 1.0 C8 B:GDP501 4.8 48.4 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Noscapine-Analogue-14E Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Noscapine-Analogue-14E Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:43.0 occ:1.00 O3G C:GTP501 1.9 41.3 1.0 O C:HOH730 2.0 40.6 1.0 O C:HOH637 2.0 39.7 1.0 O1B C:GTP501 2.0 37.2 1.0 O C:HOH655 2.1 39.2 1.0 O C:HOH648 2.1 41.9 1.0 PG C:GTP501 3.0 43.8 1.0 PB C:GTP501 3.1 39.8 1.0 O1G C:GTP501 3.5 45.2 1.0 O3B C:GTP501 3.5 50.3 1.0 O3A C:GTP501 3.5 45.8 1.0 NZ D:LYS254 3.9 52.2 1.0 OD2 C:ASP98 4.1 57.6 1.0 OE2 C:GLU71 4.1 58.0 1.0 OD1 C:ASP69 4.1 48.3 1.0 CB C:ASP98 4.2 48.0 1.0 CB C:GLN11 4.3 37.9 1.0 OD2 C:ASP69 4.3 41.4 1.0 CG C:GLU71 4.3 56.6 1.0 O2G C:GTP501 4.3 42.2 1.0 N C:GLN11 4.4 37.2 1.0 O2B C:GTP501 4.4 43.6 1.0 O1A C:GTP501 4.5 49.6 1.0 CG C:ASP98 4.6 49.6 1.0 PA C:GTP501 4.6 42.0 1.0 CG C:ASP69 4.7 51.3 1.0 CD C:GLU71 4.7 53.4 1.0 NE2 C:GLN11 4.8 50.4 1.0 CA C:GLN11 5.0 41.2 1.0 CE D:LYS254 5.0 45.9 1.0 OG1 C:THR145 5.0 43.5 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Noscapine-Analogue-14E Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Noscapine-Analogue-14E Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:79.2 occ:1.00 OE1 D:GLN11 2.0 85.7 1.0 O D:HOH601 2.0 65.7 1.0 O D:HOH652 2.1 71.7 1.0 O1A D:GDP501 2.5 98.9 1.0 O D:HOH630 2.6 70.7 1.0 CD D:GLN11 3.2 86.5 1.0 PA D:GDP501 3.9 73.3 1.0 NE2 D:GLN11 4.1 85.1 1.0 CB D:GLN11 4.1 78.8 1.0 CG D:GLN11 4.1 87.7 1.0 O D:HOH638 4.3 74.4 1.0 O2A D:GDP501 4.4 76.7 1.0 C5' D:GDP501 4.6 76.4 1.0 O1B D:GDP501 4.7 63.4 1.0 C8 D:GDP501 4.7 71.5 1.0 O5' D:GDP501 4.8 79.0 1.0 O3A D:GDP501 5.0 74.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Noscapine-Analogue-14E Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Noscapine-Analogue-14E Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:91.5 occ:1.00 OE2 F:GLU331 2.0 106.8 1.0 O1G F:ACP401 2.3 108.3 1.0 O1B F:ACP401 2.4 114.8 1.0 CD F:GLU331 2.8 99.3 1.0 OE1 F:GLU331 2.9 105.7 1.0 OD1 F:ASN333 3.2 101.0 1.0 PG F:ACP401 3.8 125.6 1.0 PB F:ACP401 3.8 120.2 1.0 ND2 F:ASN333 3.8 96.3 1.0 CG F:ASN333 3.9 95.6 1.0 CE F:LYS74 4.2 102.7 1.0 C3B F:ACP401 4.2 110.4 1.0 CG F:GLU331 4.2 85.7 1.0 O2B F:ACP401 4.5 124.4 1.0 NZ F:LYS74 4.5 116.6 1.0 O3G F:ACP401 4.6 123.6 1.0 O2G F:ACP401 4.7 102.0 1.0 O3A F:ACP401 5.0 109.7 1.0

C.Yong, S.Devine, A.C.Abel, S.Tomlins, D.Muthiah, X.G.Gao, R.Callaghan, M.Steinmetz, A.Prota, B.Capuano, P.J.Scammells. 1,3-Benzodioxole Modified Noscapine Analogues: Synthesis, Antiproliferative Activity and Tubulin Bound Structure. Chemmedchem 2021.
ISSN: ESSN 1860-7187
PubMed: 34159741
DOI: 10.1002/CMDC.202100363