Magnesium in PDB 5sbd: Tubulin-Maytansinoid-5B-Complex

The structure of Tubulin-Maytansinoid-5B-Complex, PDB code: 5sbd 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)	49.58 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.075, 158.601, 180.439, 90, 90, 90
R / Rfree (%)	17.9 / 21.4

The structure of Tubulin-Maytansinoid-5B-Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	1 atom

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

Magnesium binding site 1 out of 5 in the Tubulin-Maytansinoid-5B-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-5B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:34.9 occ:1.00 O1G A:GTP501 2.0 22.3 1.0 O A:HOH670 2.1 35.4 1.0 O A:HOH621 2.1 29.9 1.0 O A:HOH608 2.2 33.4 1.0 O A:HOH641 2.2 34.4 1.0 O1B A:GTP501 2.2 28.1 1.0 PG A:GTP501 3.2 36.9 1.0 PB A:GTP501 3.3 30.6 1.0 OE1 A:GLU71 3.5 58.5 1.0 O3B A:GTP501 3.6 45.4 1.0 O2G A:GTP501 3.7 33.0 1.0 O3A A:GTP501 3.8 43.4 1.0 NZ B:LYS254 3.9 39.8 1.0 OD1 A:ASP69 4.0 35.0 1.0 CB A:ASP98 4.2 39.2 1.0 CB A:GLN11 4.3 35.4 1.0 OD2 A:ASP69 4.3 37.3 1.0 OD2 A:ASP98 4.3 41.8 1.0 O3G A:GTP501 4.5 30.5 1.0 N A:GLN11 4.5 33.3 1.0 CG A:ASP98 4.6 41.9 1.0 O2B A:GTP501 4.6 36.1 1.0 CG A:ASP69 4.6 43.0 1.0 O1A A:GTP501 4.7 33.5 1.0 CD A:GLU71 4.7 53.8 1.0 PA A:GTP501 4.8 32.9 1.0 OE1 A:GLN11 4.8 54.6 1.0 CE B:LYS254 5.0 42.7 1.0 CA A:GLN11 5.0 37.0 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Maytansinoid-5B-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-5B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:26.3 occ:1.00 O B:HOH681 2.0 28.6 1.0 OE1 B:GLN11 2.1 35.9 1.0 O1A B:GDP501 2.2 35.0 1.0 O C:HOH713 2.3 41.3 1.0 O B:HOH699 2.4 38.9 1.0 O B:HOH609 2.6 44.8 1.0 O B:HOH780 3.2 59.1 1.0 CD B:GLN11 3.3 52.3 1.0 PA B:GDP501 3.6 31.6 1.0 O3A B:GDP501 4.0 33.6 1.0 OD2 B:ASP179 4.0 37.7 1.0 CB B:GLN11 4.1 33.5 1.0 CG B:GLN11 4.2 40.7 1.0 OD1 B:ASN101 4.3 33.7 1.0 NE2 B:GLN11 4.3 43.2 1.0 C5' B:GDP501 4.4 33.4 1.0 O5' B:GDP501 4.5 32.2 1.0 O1B B:GDP501 4.5 27.4 1.0 O2A B:GDP501 4.6 34.2 1.0 OE1 C:GLU254 4.6 39.5 1.0 O C:HOH637 4.7 50.6 1.0 PB B:GDP501 4.9 31.7 1.0 C8 B:GDP501 5.0 39.7 1.0 CG B:ASP179 5.0 44.4 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Maytansinoid-5B-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-5B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:29.8 occ:1.00 O C:HOH764 2.0 33.5 1.0 O C:HOH657 2.0 29.1 1.0 O1G C:GTP501 2.1 28.9 1.0 O C:HOH673 2.1 32.4 1.0 O1B C:GTP501 2.1 28.1 1.0 O C:HOH674 2.1 32.1 1.0 PB C:GTP501 3.2 27.5 1.0 PG C:GTP501 3.2 31.8 1.0 O3B C:GTP501 3.6 39.0 1.0 O3A C:GTP501 3.6 38.0 1.0 O2G C:GTP501 3.7 34.3 1.0 NZ D:LYS254 3.9 33.7 1.0 OE2 C:GLU71 3.9 46.8 1.0 OD1 C:ASP69 4.1 29.9 1.0 CG C:GLU71 4.2 35.1 1.0 CB C:GLN11 4.2 28.9 1.0 OD2 C:ASP69 4.3 30.0 1.0 OD2 C:ASP98 4.3 41.3 1.0 CB C:ASP98 4.4 32.5 1.0 N C:GLN11 4.4 27.7 1.0 O3G C:GTP501 4.5 31.5 1.0 O2B C:GTP501 4.5 33.0 1.0 CD C:GLU71 4.6 40.3 1.0 O C:HOH626 4.6 41.2 1.0 CG C:ASP69 4.6 35.4 1.0 NE2 C:GLN11 4.7 39.0 1.0 PA C:GTP501 4.7 30.3 1.0 CG C:ASP98 4.7 35.5 1.0 O1A C:GTP501 4.7 35.2 1.0 CA C:GLN11 5.0 28.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Maytansinoid-5B-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-5B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:65.3 occ:1.00 O D:HOH608 2.1 56.1 1.0 OE1 D:GLN11 2.2 77.6 1.0 O D:HOH700 2.2 68.2 1.0 O1A D:GDP501 2.3 79.1 1.0 O D:HOH657 2.8 56.2 1.0 CD D:GLN11 3.3 81.4 1.0 PA D:GDP501 3.8 56.2 1.0 NE2 D:GLN11 4.2 78.6 1.0 CB D:GLN11 4.2 65.2 1.0 CG D:GLN11 4.3 71.2 1.0 C5' D:GDP501 4.4 57.1 1.0 O2A D:GDP501 4.5 59.6 1.0 O5' D:GDP501 4.6 54.8 1.0 O3A D:GDP501 4.7 52.3 1.0 O1B D:GDP501 4.7 55.5 1.0 C8 D:GDP501 4.9 57.1 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Maytansinoid-5B-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-5B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:74.6 occ:1.00 O1B F:ACP401 2.3 93.3 1.0 OE2 F:GLU331 2.3 88.7 1.0 O3G F:ACP401 2.4 89.0 1.0 CD F:GLU331 3.1 84.0 1.0 OE1 F:GLU331 3.1 90.1 1.0 OD1 F:ASN333 3.3 88.7 1.0 NZ F:LYS74 3.6 81.1 1.0 PB F:ACP401 3.6 96.1 1.0 PG F:ACP401 3.7 106.2 1.0 O2B F:ACP401 4.0 101.8 1.0 O2G F:ACP401 4.1 86.2 1.0 CG F:ASN333 4.1 78.6 1.0 ND2 F:ASN333 4.2 78.7 1.0 C3B F:ACP401 4.3 91.3 1.0 O F:HOH544 4.4 70.2 1.0 CG F:GLU331 4.5 67.1 1.0 CE F:LYS74 4.8 77.0 1.0 O3A F:ACP401 4.9 87.9 1.0 O F:HOH542 5.0 66.2 1.0 O1G F:ACP401 5.0 93.5 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