Magnesium in PDB 6fjm: Tubulin-Disorazole Z Complex

The structure of Tubulin-Disorazole Z Complex, PDB code: 6fjm was solved by G.Menchon, A.E.Prota, D.Lucena Agell, P.Bucher, R.Jansen, H.Irschik, R.Mueller, I.Paterson, J.F.Diaz, K.-H.Altmann, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.97 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.390, 157.630, 179.630, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.3

The structure of Tubulin-Disorazole Z Complex also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Magnesium atom in the Tubulin-Disorazole Z Complex (pdb code 6fjm). 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-Disorazole Z Complex, PDB code: 6fjm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Disorazole Z Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:38.9 occ:1.00 O2G A:GTP501 2.1 36.5 1.0 O A:HOH614 2.1 38.8 1.0 O A:HOH658 2.1 34.4 1.0 O1B A:GTP501 2.2 36.1 1.0 O A:HOH645 2.2 35.2 1.0 O A:HOH644 2.3 44.2 1.0 PG A:GTP501 3.2 38.4 1.0 PB A:GTP501 3.3 39.6 1.0 O3B A:GTP501 3.6 52.5 1.0 NZ B:LYS254 3.7 52.7 1.0 O3A A:GTP501 3.7 44.9 1.0 O1G A:GTP501 3.8 37.5 1.0 OE2 A:GLU71 4.0 66.9 1.0 OD1 A:ASP69 4.1 52.3 1.0 CB A:GLN11 4.1 37.0 1.0 OD2 A:ASP69 4.3 48.8 1.0 N A:GLN11 4.3 42.7 1.0 CG A:GLU71 4.4 66.0 1.0 OD2 A:ASP98 4.4 54.1 1.0 O1A A:GTP501 4.4 37.6 1.0 CB A:ASP98 4.5 44.4 1.0 O3G A:GTP501 4.5 35.5 1.0 O2B A:GTP501 4.6 42.6 1.0 PA A:GTP501 4.6 39.3 1.0 CG A:ASP69 4.6 56.9 1.0 CD A:GLU71 4.7 65.2 1.0 NE2 A:GLN11 4.7 50.9 1.0 CG A:ASP98 4.8 50.3 1.0 CE B:LYS254 4.8 43.3 1.0 CA A:GLN11 4.8 44.3 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Disorazole Z Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:33.7 occ:1.00 OE1 B:GLN11 2.1 51.4 1.0 O B:HOH619 2.1 46.7 1.0 O C:HOH693 2.2 55.8 1.0 O1A B:GDP501 2.3 39.1 1.0 O B:HOH667 2.4 43.6 1.0 O B:HOH610 2.6 42.4 1.0 CD B:GLN11 3.3 47.6 1.0 O B:HOH740 3.4 65.3 1.0 PA B:GDP501 3.5 37.5 1.0 O3A B:GDP501 3.7 45.2 1.0 OD2 B:ASP179 3.9 48.5 1.0 CB B:GLN11 4.0 35.9 1.0 CG B:GLN11 4.1 38.6 1.0 NE2 B:GLN11 4.3 48.9 1.0 C5' B:GDP501 4.3 40.8 1.0 O5' B:GDP501 4.3 42.0 1.0 ND2 B:ASN101 4.4 40.1 1.0 O C:HOH683 4.4 63.2 1.0 OE1 C:GLU254 4.5 50.5 1.0 O1B B:GDP501 4.6 33.1 1.0 O2A B:GDP501 4.7 37.1 1.0 PB B:GDP501 4.8 36.3 1.0 C8 B:GDP501 4.8 38.9 1.0 CG B:ASP179 4.9 48.0 1.0 OD1 B:ASN101 4.9 44.7 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Disorazole Z Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:34.0 occ:1.00 O1G C:GTP501 2.0 33.0 1.0 O C:HOH661 2.0 33.7 1.0 O C:HOH737 2.1 32.3 1.0 O C:HOH630 2.1 39.4 1.0 O1B C:GTP501 2.1 31.3 1.0 O C:HOH653 2.2 35.2 1.0 PG C:GTP501 3.1 39.0 1.0 PB C:GTP501 3.1 31.8 1.0 O3B C:GTP501 3.5 42.4 1.0 O2G C:GTP501 3.5 40.3 1.0 O3A C:GTP501 3.7 42.5 1.0 NZ D:LYS254 3.9 45.0 1.0 OD1 C:ASP69 4.1 49.2 1.0 OE2 C:GLU71 4.1 56.3 1.0 OD2 C:ASP98 4.3 48.4 1.0 CB C:GLN11 4.3 29.0 1.0 CG C:GLU71 4.3 53.4 1.0 OD2 C:ASP69 4.3 38.0 1.0 CB C:ASP98 4.4 42.5 1.0 O3G C:GTP501 4.4 31.6 1.0 N C:GLN11 4.4 31.6 1.0 O2B C:GTP501 4.4 36.7 1.0 O1A C:GTP501 4.6 37.6 1.0 CG C:ASP69 4.6 42.1 1.0 CG C:ASP98 4.7 42.7 1.0 CD C:GLU71 4.7 56.7 1.0 PA C:GTP501 4.7 34.4 1.0 O C:HOH811 4.8 87.2 1.0 NE2 C:GLN11 4.9 46.4 1.0 CA C:GLN11 5.0 36.6 1.0 CE D:LYS254 5.0 42.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Disorazole Z Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:51.3 occ:1.00 OE1 D:GLN11 1.9 81.0 1.0 O D:HOH618 2.0 51.8 1.0 O D:HOH707 2.3 60.4 1.0 O1A D:GDP501 2.3 65.9 1.0 O D:HOH663 2.9 66.4 1.0 CD D:GLN11 3.1 74.3 1.0 PA D:GDP501 3.8 60.3 1.0 CG D:GLN11 4.0 69.4 1.0 CB D:GLN11 4.0 69.2 1.0 NE2 D:GLN11 4.0 64.9 1.0 O3A D:GDP501 4.3 55.4 1.0 C5' D:GDP501 4.5 60.7 1.0 C8 D:GDP501 4.6 56.6 1.0 O2A D:GDP501 4.6 62.5 1.0 O5' D:GDP501 4.7 64.6 1.0 O1B D:GDP501 4.8 50.5 1.0 OD1 D:ASN101 5.0 77.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Disorazole Z Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:0.1 occ:1.00 OE2 F:GLU331 2.6 0.8 1.0 O1G F:ACP401 2.7 1.0 1.0 O1B F:ACP401 2.7 0.0 1.0 OD1 F:ASN333 2.7 0.3 1.0 OE1 F:GLU331 2.9 0.1 1.0 CD F:GLU331 3.1 98.3 1.0 NZ F:LYS74 3.3 98.8 1.0 CG F:ASN333 3.8 89.9 1.0 PB F:ACP401 3.9 0.1 1.0 PG F:ACP401 3.9 0.8 1.0 O F:HOH513 4.2 81.9 1.0 ND2 F:ASN333 4.2 92.4 1.0 C3B F:ACP401 4.2 0.8 1.0 O2B F:ACP401 4.3 0.6 1.0 CE F:LYS74 4.5 92.6 1.0 CG F:GLU331 4.7 80.2 1.0 O3G F:ACP401 4.7 0.1 1.0 O F:HOH523 4.8 85.3 1.0

G.Menchon, A.E.Prota, D.Lucena-Agell, P.Bucher, R.Jansen, H.Irschik, R.Muller, I.Paterson, J.F.Diaz, K.H.Altmann, M.O.Steinmetz. A Fluorescence Anisotropy Assay to Discover and Characterize Ligands Targeting the Maytansine Site of Tubulin. Nat Commun V. 9 2106 2018.
ISSN: ESSN 2041-1723
PubMed: 29844393
DOI: 10.1038/S41467-018-04535-8