Magnesium in PDB 5sb9: Tubulin-Maytansinoid-4A-Complex

The structure of Tubulin-Maytansinoid-4A-Complex, PDB code: 5sb9 was solved by P.Marzullo, Z.Boiarska, H.Perez-Pena, A.-C.Abel, B.Alvarez-Bernad, D.Lucena-Agell, F.Vasile, M.Sironi, M.O.Steinmetz, A.E.Prota, J.F.Diaz, S.Pieraccini, D.Passarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.92 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.539, 156.717, 181.697, 90, 90, 90
R / Rfree (%)	19.4 / 22.7

The structure of Tubulin-Maytansinoid-4A-Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	3 atoms

The binding sites of Magnesium atom in the Tubulin-Maytansinoid-4A-Complex (pdb code 5sb9). 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-Maytansinoid-4A-Complex, PDB code: 5sb9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Maytansinoid-4A-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Maytansinoid-4A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.2 occ:1.00 O3G A:GTP501 2.0 35.5 1.0 O A:HOH604 2.0 40.0 1.0 O A:HOH615 2.0 45.3 1.0 O A:HOH631 2.1 46.6 1.0 O A:HOH601 2.1 44.9 1.0 O1B A:GTP501 2.2 39.5 1.0 PG A:GTP501 3.2 44.8 1.0 PB A:GTP501 3.2 42.1 1.0 OE1 A:GLU71 3.4 71.8 1.0 O3B A:GTP501 3.5 53.2 1.0 O3A A:GTP501 3.7 49.4 1.0 NZ B:LYS254 3.8 45.3 1.0 O2G A:GTP501 3.8 39.8 1.0 CB A:GLN11 4.2 42.9 1.0 OD1 A:ASP69 4.3 48.5 1.0 OD2 A:ASP98 4.3 54.1 1.0 O1G A:GTP501 4.4 36.1 1.0 CB A:ASP98 4.4 51.0 1.0 N A:GLN11 4.5 48.2 1.0 O1A A:GTP501 4.5 43.1 1.0 O2B A:GTP501 4.5 49.4 1.0 NE2 A:GLN11 4.6 54.8 1.0 CG A:ASP98 4.6 47.4 1.0 CD A:GLU71 4.6 72.5 1.0 OD2 A:ASP69 4.6 63.0 1.0 PA A:GTP501 4.7 45.1 1.0 CB A:GLU71 4.9 64.6 1.0 CG A:ASP69 4.9 56.7 1.0 CE B:LYS254 4.9 44.0 1.0 CA A:GLN11 5.0 43.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Maytansinoid-4A-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Maytansinoid-4A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:35.5 occ:1.00 O B:HOH620 2.0 39.5 1.0 OE1 B:GLN11 2.1 51.5 1.0 O B:HOH639 2.2 38.9 1.0 O C:HOH664 2.2 46.3 1.0 O1A B:GDP501 2.4 39.3 1.0 O B:HOH613 2.8 53.9 1.0 CD B:GLN11 3.3 49.1 1.0 OD2 B:ASP179 3.4 49.3 1.0 PA B:GDP501 3.7 36.4 1.0 O3A B:GDP501 3.9 41.1 1.0 C5' B:GDP501 4.2 40.1 1.0 CB B:GLN11 4.2 41.9 1.0 NE2 B:GLN11 4.2 51.8 1.0 OD1 B:ASN101 4.2 43.9 1.0 CG B:GLN11 4.3 49.0 1.0 O5' B:GDP501 4.4 33.0 1.0 CG B:ASP179 4.5 50.2 1.0 OE1 C:GLU254 4.7 45.2 1.0 C8 B:GDP501 4.7 40.1 1.0 O2A B:GDP501 4.8 37.1 1.0 O1B B:GDP501 4.9 36.5 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Maytansinoid-4A-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Maytansinoid-4A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:38.9 occ:1.00 O C:HOH644 1.9 41.6 1.0 O C:HOH615 2.0 33.2 1.0 O C:HOH625 2.0 34.4 1.0 O1G C:GTP501 2.0 30.4 1.0 O C:HOH617 2.1 37.8 1.0 O2B C:GTP501 2.1 43.6 1.0 PB C:GTP501 3.2 37.5 1.0 PG C:GTP501 3.2 43.5 1.0 O3B C:GTP501 3.6 41.6 1.0 O3A C:GTP501 3.6 49.4 1.0 O2G C:GTP501 3.8 35.4 1.0 OE2 C:GLU71 3.8 54.9 1.0 NZ D:LYS254 3.9 45.7 1.0 OD1 C:ASP69 4.2 39.1 1.0 CG C:GLU71 4.2 45.1 1.0 CB C:GLN11 4.3 37.1 1.0 OD2 C:ASP98 4.3 48.0 1.0 OD2 C:ASP69 4.3 38.3 1.0 O3G C:GTP501 4.5 36.3 1.0 CB C:ASP98 4.5 41.1 1.0 O1B C:GTP501 4.5 43.5 1.0 N C:GLN11 4.5 36.0 1.0 CD C:GLU71 4.5 48.4 1.0 OE1 C:GLN11 4.7 55.3 1.0 CG C:ASP69 4.7 41.8 1.0 PA C:GTP501 4.8 40.5 1.0 O1A C:GTP501 4.8 35.4 1.0 CG C:ASP98 4.9 44.0 1.0 CA C:GLN11 5.0 38.4 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Maytansinoid-4A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:73.2 occ:1.00 O D:HOH622 1.9 75.1 1.0 O1A D:GDP501 2.2 68.7 1.0 OE1 D:GLN11 2.3 95.9 1.0 O D:HOH609 2.3 72.8 1.0 CD D:GLN11 2.6 85.1 1.0 NE2 D:GLN11 2.9 85.2 1.0 O D:HOH629 3.0 73.3 1.0 CG D:GLN11 3.6 86.8 1.0 PA D:GDP501 3.6 68.4 1.0 CB D:GLN11 3.6 78.7 1.0 O3A D:GDP501 4.0 69.0 1.0 C5' D:GDP501 4.2 73.0 1.0 O5' D:GDP501 4.4 70.6 1.0 O1B D:GDP501 4.5 74.6 1.0 O2A D:GDP501 4.7 76.8 1.0 C8 D:GDP501 4.7 68.0 1.0 OD1 D:ASN101 4.8 110.7 1.0 PB D:GDP501 4.9 64.0 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Maytansinoid-4A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:111.6 occ:1.00 OE2 F:GLU331 2.6 111.6 1.0 ND2 F:ASN333 2.9 102.7 1.0 O1B F:ACP501 3.1 130.1 1.0 O3G F:ACP501 3.4 102.3 1.0 CD F:GLU331 3.6 106.1 1.0 O1G F:ACP501 3.9 117.5 1.0 OE1 F:GLU331 4.0 112.0 1.0 PG F:ACP501 4.2 136.6 1.0 CG F:ASN333 4.2 96.0 1.0 PB F:ACP501 4.3 138.6 1.0 NZ F:LYS74 4.5 106.5 1.0 O2B F:ACP501 4.5 129.1 1.0 C3B F:ACP501 4.8 130.1 1.0 OD1 F:ASN333 4.8 101.9 1.0 CG F:GLU331 5.0 83.9 1.0

P.Marzullo, Z.Boiarska, H.Perez-Pena, A.C.Abel, B.Alvarez-Bernad, D.Lucena-Agell, F.Vasile, M.Sironi, K.H.Altmann, A.E.Prota, J.F.Diaz, S.Pieraccini, D.Passarella. Maytansinol Derivatives: Side Reactions As A Chance For New Tubulin Binders. Chemistry 2021.
ISSN: ISSN 0947-6539
PubMed: 34788896
DOI: 10.1002/CHEM.202103520