Magnesium in PDB 6fjf: Tubulin-Fcmaytansine Complex

The structure of Tubulin-Fcmaytansine Complex, PDB code: 6fjf was solved by G.Menchon, A.E.Prota, D.Lucena Angell, P.Bucher, 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)	49.55 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.373, 156.739, 180.956, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.8

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

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Fcmaytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.9 occ:1.00 O A:HOH650 2.0 35.4 1.0 O2G A:GTP501 2.0 33.6 1.0 O A:HOH616 2.1 31.4 1.0 O A:HOH632 2.1 40.9 1.0 O1B A:GTP501 2.2 36.1 1.0 O A:HOH618 2.2 33.7 1.0 PG A:GTP501 3.2 35.9 1.0 PB A:GTP501 3.3 38.4 1.0 O3B A:GTP501 3.6 49.4 1.0 O1G A:GTP501 3.6 37.7 1.0 O3A A:GTP501 3.7 45.4 1.0 NZ B:LYS254 3.9 52.6 1.0 CB A:GLN11 4.1 45.6 1.0 OD1 A:ASP69 4.2 49.6 1.0 OD2 A:ASP98 4.3 48.7 1.0 OD2 A:ASP69 4.4 41.9 1.0 N A:GLN11 4.4 41.2 1.0 CB A:ASP98 4.4 40.9 1.0 O3G A:GTP501 4.5 37.2 1.0 OE1 A:GLN11 4.5 49.9 1.0 OE2 A:GLU71 4.5 54.3 1.0 O2B A:GTP501 4.6 47.5 1.0 O1A A:GTP501 4.6 32.5 1.0 PA A:GTP501 4.7 37.8 1.0 CB A:GLU71 4.8 65.3 1.0 CG A:ASP69 4.8 47.4 1.0 CG A:ASP98 4.8 47.0 1.0 CE B:LYS254 4.8 42.9 1.0 CA A:GLN11 4.9 46.5 1.0 O B:HOH618 4.9 55.6 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Fcmaytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:34.4 occ:1.00 O B:HOH612 2.0 49.2 1.0 O B:HOH626 2.2 33.4 1.0 OE1 B:GLN11 2.2 55.0 1.0 O1A B:GDP501 2.2 35.6 1.0 O C:HOH621 2.3 44.2 1.0 O B:HOH638 2.4 47.0 1.0 CD B:GLN11 3.4 48.1 1.0 PA B:GDP501 3.6 36.8 1.0 OD2 B:ASP179 3.9 49.7 1.0 O3A B:GDP501 4.0 38.7 1.0 OD1 B:ASN101 4.1 45.0 1.0 CB B:GLN11 4.1 31.1 1.0 CG B:GLN11 4.3 36.6 1.0 NE2 B:GLN11 4.4 45.7 1.0 O1B B:GDP501 4.4 33.9 1.0 C5' B:GDP501 4.5 29.5 1.0 OE1 C:GLU254 4.5 49.3 1.0 O5' B:GDP501 4.5 33.6 1.0 O2A B:GDP501 4.6 32.5 1.0 PB B:GDP501 4.8 35.2 1.0 ND2 B:ASN101 4.8 33.5 1.0 CG B:ASN101 4.9 40.8 1.0 CG B:ASP179 4.9 53.6 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Fcmaytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:30.9 occ:1.00 O C:HOH654 1.9 29.0 1.0 O1B C:GTP501 2.0 37.3 1.0 O C:HOH674 2.1 35.9 1.0 O1G C:GTP501 2.1 27.0 1.0 O C:HOH611 2.1 37.1 1.0 O C:HOH705 2.1 30.9 1.0 PG C:GTP501 3.2 38.5 1.0 PB C:GTP501 3.2 33.1 1.0 O3B C:GTP501 3.6 43.4 1.0 O2G C:GTP501 3.6 37.1 1.0 O3A C:GTP501 3.8 39.8 1.0 OE2 C:GLU71 3.9 65.1 1.0 NZ D:LYS254 4.0 37.9 1.0 OD1 C:ASP69 4.0 36.2 1.0 CG C:GLU71 4.1 50.2 1.0 CB C:GLN11 4.2 28.6 1.0 OD2 C:ASP69 4.2 35.2 1.0 CB C:ASP98 4.4 31.2 1.0 CD C:GLU71 4.4 61.1 1.0 N C:GLN11 4.4 29.1 1.0 OD2 C:ASP98 4.4 39.9 1.0 O2B C:GTP501 4.5 32.1 1.0 O3G C:GTP501 4.5 31.4 1.0 CG C:ASP69 4.6 33.7 1.0 O C:HOH678 4.6 52.9 1.0 O1A C:GTP501 4.7 28.1 1.0 OE1 C:GLN11 4.7 38.4 1.0 CG C:ASP98 4.7 38.3 1.0 PA C:GTP501 4.8 31.8 1.0 CA C:GLN11 4.9 30.2 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Fcmaytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:52.3 occ:1.00 O D:HOH607 2.0 48.6 1.0 O1A D:GDP501 2.3 82.4 1.0 O D:HOH649 2.3 51.9 1.0 NE2 D:GLN11 2.4 55.1 1.0 O D:HOH669 3.3 53.8 1.0 PA D:GDP501 3.5 70.2 1.0 CD D:GLN11 3.7 67.0 1.0 O3A D:GDP501 3.7 67.2 1.0 ND2 D:ASN101 3.7 86.1 1.0 C5' D:GDP501 4.3 55.4 1.0 CB D:GLN11 4.3 58.6 1.0 O5' D:GDP501 4.4 62.9 1.0 OE1 D:GLN11 4.4 70.8 1.0 O1B D:GDP501 4.6 42.3 1.0 CG D:GLN11 4.6 62.5 1.0 O2A D:GDP501 4.6 59.0 1.0 OD2 D:ASP179 4.6 0.2 1.0 PB D:GDP501 4.7 66.5 1.0 CG D:ASN101 4.7 80.5 1.0 OD1 D:ASN101 4.9 70.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Fcmaytansine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Fcmaytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:97.9 occ:1.00 O2G F:ACP401 2.2 0.9 1.0 OE2 F:GLU331 2.3 84.3 1.0 O1B F:ACP401 2.7 0.9 1.0 NZ F:LYS74 3.0 86.5 1.0 ND2 F:ASN333 3.1 99.0 1.0 CD F:GLU331 3.3 77.4 1.0 PG F:ACP401 3.6 0.9 1.0 OE1 F:GLU331 3.7 83.5 1.0 PB F:ACP401 3.8 0.1 1.0 O1G F:ACP401 3.9 0.2 1.0 OE2 A:GLU450 4.1 0.4 1.0 O2B F:ACP401 4.2 0.1 1.0 CG F:ASN333 4.3 98.1 1.0 C3B F:ACP401 4.3 1.0 1.0 CE F:LYS74 4.4 82.4 1.0 CD A:GLU450 4.5 0.4 1.0 CG A:GLU450 4.5 0.1 1.0 CG F:GLU331 4.6 67.7 1.0 OD1 F:ASN333 4.7 0.9 1.0 O3G F:ACP401 4.8 0.9 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