Magnesium in PDB 5sbb: Tubulin-Maytansinoid-4C-Complex

The structure of Tubulin-Maytansinoid-4C-Complex, PDB code: 5sbb 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)	49.54 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.615, 157.484, 180.633, 90, 90, 90
R / Rfree (%)	18.3 / 22.8

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

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

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

Magnesium binding site 1 out of 5 in the Tubulin-Maytansinoid-4C-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-4C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:32.4 occ:1.00 O1G A:GTP501 2.0 31.4 1.0 O A:HOH629 2.0 31.6 1.0 O A:HOH689 2.1 37.3 1.0 O A:HOH649 2.2 35.9 1.0 O1B A:GTP501 2.2 29.9 1.0 O A:HOH648 2.2 36.1 1.0 PG A:GTP501 3.2 38.6 1.0 PB A:GTP501 3.3 36.2 1.0 O3B A:GTP501 3.6 48.6 1.0 O2G A:GTP501 3.7 34.1 1.0 O3A A:GTP501 3.8 45.8 1.0 OE1 A:GLU71 3.8 55.6 1.0 NZ B:LYS254 3.9 43.5 1.0 OD1 A:ASP69 4.0 39.1 1.0 CB A:GLN11 4.2 35.3 1.0 OD2 A:ASP98 4.3 38.8 1.0 OD2 A:ASP69 4.3 40.5 1.0 CB A:ASP98 4.3 38.8 1.0 N A:GLN11 4.4 35.7 1.0 O3G A:GTP501 4.4 32.8 1.0 O2B A:GTP501 4.6 37.2 1.0 CG A:ASP69 4.6 41.0 1.0 CG A:ASP98 4.7 38.8 1.0 OE1 A:GLN11 4.8 52.0 1.0 O1A A:GTP501 4.8 42.2 1.0 PA A:GTP501 4.8 36.5 1.0 CA A:GLN11 4.9 36.9 1.0 CB A:GLU71 4.9 62.7 1.0 CD A:GLU71 5.0 60.7 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Maytansinoid-4C-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-4C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:30.2 occ:1.00 O B:HOH677 2.0 34.2 1.0 OE1 B:GLN11 2.1 42.5 1.0 O1A B:GDP501 2.2 42.3 1.0 O B:HOH699 2.3 42.5 1.0 O C:HOH694 2.3 47.9 1.0 O B:HOH611 2.6 42.9 1.0 O B:HOH761 3.0 57.8 1.0 CD B:GLN11 3.3 46.7 1.0 PA B:GDP501 3.6 32.2 1.0 OD2 B:ASP179 3.9 45.3 1.0 CB B:GLN11 4.1 36.4 1.0 O3A B:GDP501 4.1 37.5 1.0 NE2 B:GLN11 4.2 52.4 1.0 OD1 B:ASN101 4.2 37.2 1.0 CG B:GLN11 4.2 40.9 1.0 O C:HOH656 4.5 60.9 1.0 C5' B:GDP501 4.5 38.5 1.0 O1B B:GDP501 4.5 28.3 1.0 O5' B:GDP501 4.6 35.1 1.0 O2A B:GDP501 4.6 31.9 1.0 OE1 C:GLU254 4.7 46.5 1.0 O C:HOH867 4.9 60.4 1.0 ND2 B:ASN101 4.9 35.6 1.0 PB B:GDP501 5.0 32.5 1.0 CG B:ASP179 5.0 46.8 1.0 CG B:ASN101 5.0 40.0 1.0 C8 B:GDP501 5.0 34.3 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Maytansinoid-4C-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-4C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:31.6 occ:1.00 O1G C:GTP501 2.0 27.9 1.0 O C:HOH640 2.0 37.5 1.0 O C:HOH728 2.1 31.4 1.0 O1B C:GTP501 2.1 29.3 1.0 O C:HOH657 2.1 32.2 1.0 O C:HOH690 2.2 37.8 1.0 PG C:GTP501 3.1 35.5 1.0 PB C:GTP501 3.1 30.7 1.0 O3B C:GTP501 3.5 42.9 1.0 O3A C:GTP501 3.6 41.8 1.0 O2G C:GTP501 3.6 33.6 1.0 NZ D:LYS254 4.0 39.6 1.0 OD1 C:ASP69 4.0 35.3 1.0 OE2 C:GLU71 4.0 47.0 1.0 CG C:GLU71 4.2 39.7 1.0 CB C:GLN11 4.3 32.5 1.0 OD2 C:ASP69 4.3 33.5 1.0 CB C:ASP98 4.3 36.3 1.0 O3G C:GTP501 4.4 31.8 1.0 N C:GLN11 4.4 31.3 1.0 O2B C:GTP501 4.4 34.1 1.0 OD2 C:ASP98 4.5 43.0 1.0 O C:HOH637 4.5 45.5 1.0 CG C:ASP69 4.6 37.4 1.0 CD C:GLU71 4.6 44.4 1.0 NE2 C:GLN11 4.7 45.9 1.0 PA C:GTP501 4.7 30.7 1.0 O1A C:GTP501 4.7 34.0 1.0 CG C:ASP98 4.8 40.6 1.0 O C:HOH650 4.9 61.3 1.0 CA C:GLN11 4.9 31.7 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Maytansinoid-4C-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-4C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:58.6 occ:1.00 O D:HOH609 2.1 53.2 1.0 OE1 D:GLN11 2.1 72.1 1.0 O D:HOH655 2.3 57.0 1.0 O1A D:GDP501 2.3 89.5 1.0 O D:HOH668 2.8 66.2 1.0 CD D:GLN11 3.3 76.5 1.0 PA D:GDP501 3.7 60.2 1.0 O2A D:GDP501 3.9 55.3 1.0 CB D:GLN11 4.0 61.6 1.0 CG D:GLN11 4.2 71.5 1.0 NE2 D:GLN11 4.3 80.1 1.0 O1B D:GDP501 4.3 59.4 1.0 O D:HOH699 4.5 55.4 1.0 O3B D:GDP501 4.7 83.2 1.0 C5' D:GDP501 4.7 61.8 1.0 O3A D:GDP501 4.7 73.0 1.0 O5' D:GDP501 4.7 61.6 1.0 PB D:GDP501 4.8 56.8 1.0 OD1 D:ASN101 5.0 67.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Maytansinoid-4C-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-4C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:85.8 occ:1.00 O1B F:ACP401 2.2 103.8 1.0 OE2 F:GLU331 2.3 91.6 1.0 O3G F:ACP401 2.4 93.5 1.0 OD1 F:ASN333 3.0 97.9 1.0 CD F:GLU331 3.1 90.3 1.0 OE1 F:GLU331 3.3 99.4 1.0 NZ F:LYS74 3.7 100.9 1.0 PB F:ACP401 3.7 103.3 1.0 PG F:ACP401 3.7 113.1 1.0 CG F:ASN333 3.9 88.4 1.0 O2G F:ACP401 4.1 89.9 1.0 ND2 F:ASN333 4.2 86.8 1.0 O2B F:ACP401 4.3 108.0 1.0 C3B F:ACP401 4.3 95.4 1.0 CG F:GLU331 4.6 69.4 1.0 O3A F:ACP401 4.8 90.7 1.0 CE F:LYS74 4.9 87.5 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