Magnesium in PDB 5sbe: Tubulin-Maytansinoid-5C-Complex

The structure of Tubulin-Maytansinoid-5C-Complex, PDB code: 5sbe 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)	48.06 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.118, 158.404, 181.377, 90, 90, 90
R / Rfree (%)	19.2 / 23

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

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

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

Magnesium binding site 1 out of 5 in the Tubulin-Maytansinoid-5C-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-5C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:52.2 occ:1.00 O A:HOH610 2.0 57.8 1.0 O1G A:GTP501 2.1 42.9 1.0 O A:HOH615 2.1 54.5 1.0 O A:HOH605 2.2 57.1 1.0 O A:HOH624 2.2 59.8 1.0 O1B A:GTP501 2.2 45.5 1.0 PG A:GTP501 3.3 47.9 1.0 PB A:GTP501 3.4 51.8 1.0 OE1 A:GLU71 3.4 80.1 1.0 O3B A:GTP501 3.7 53.7 1.0 O2G A:GTP501 3.9 51.9 1.0 O3A A:GTP501 4.0 60.4 1.0 OD1 A:ASP69 4.1 57.5 1.0 NZ B:LYS254 4.1 61.4 1.0 CD A:GLU71 4.2 70.1 1.0 CB A:GLN11 4.2 53.3 1.0 OE2 A:GLU71 4.4 74.9 1.0 CB A:ASP98 4.4 55.9 1.0 N A:GLN11 4.5 51.9 1.0 NE2 A:GLN11 4.5 56.2 1.0 OD2 A:ASP69 4.5 65.5 1.0 O3G A:GTP501 4.6 47.3 1.0 O2B A:GTP501 4.6 53.9 1.0 CG A:ASP69 4.7 64.2 1.0 O1A A:GTP501 4.8 46.9 1.0 PA A:GTP501 4.9 51.4 1.0 CG A:ASP98 4.9 58.5 1.0 CA A:GLN11 5.0 52.5 1.0 OG1 A:THR145 5.0 51.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Maytansinoid-5C-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-5C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:49.5 occ:1.00 O B:HOH603 2.0 45.5 1.0 O1A B:GDP501 2.1 55.3 1.0 O C:HOH647 2.2 38.8 1.0 O B:HOH658 2.3 48.0 1.0 OE1 B:GLN11 2.3 44.6 1.0 O B:HOH628 2.3 41.8 1.0 CD B:GLN11 3.5 46.5 1.0 PA B:GDP501 3.5 48.4 1.0 OD1 B:ASN101 4.0 45.9 1.0 O2A B:GDP501 4.1 41.7 1.0 CB B:GLN11 4.2 45.7 1.0 OD2 B:ASP179 4.3 54.0 1.0 O3B B:GDP501 4.3 48.4 1.0 NE2 B:GLN11 4.4 49.9 1.0 CG B:GLN11 4.4 51.8 1.0 O3A B:GDP501 4.5 56.0 1.0 C5' B:GDP501 4.5 40.2 1.0 O5' B:GDP501 4.5 34.2 1.0 OE1 C:GLU254 4.6 48.3 1.0 O1B B:GDP501 4.6 41.5 1.0 PB B:GDP501 4.7 44.8 1.0 O C:HOH683 4.7 46.5 1.0 CG B:ASN101 4.9 46.6 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Maytansinoid-5C-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-5C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.7 occ:1.00 O1G C:GTP501 2.1 43.3 1.0 O C:HOH622 2.1 41.1 1.0 O C:HOH618 2.1 41.5 1.0 O C:HOH650 2.1 41.2 1.0 O1B C:GTP501 2.2 42.2 1.0 O C:HOH638 2.3 52.7 1.0 PB C:GTP501 3.3 40.1 1.0 PG C:GTP501 3.3 42.9 1.0 O3B C:GTP501 3.7 41.7 1.0 O3A C:GTP501 3.7 51.4 1.0 OE2 C:GLU71 3.9 52.8 1.0 NZ D:LYS254 3.9 55.1 1.0 O2G C:GTP501 3.9 42.8 1.0 CG C:GLU71 4.1 48.5 1.0 CB C:GLN11 4.3 44.4 1.0 OD1 C:ASP69 4.3 41.7 1.0 OD2 C:ASP69 4.4 44.5 1.0 CB C:ASP98 4.4 46.4 1.0 CD C:GLU71 4.5 50.6 1.0 NE2 C:GLN11 4.5 55.0 1.0 O3G C:GTP501 4.5 41.5 1.0 O2B C:GTP501 4.6 40.9 1.0 N C:GLN11 4.6 41.0 1.0 O1A C:GTP501 4.8 48.2 1.0 PA C:GTP501 4.8 43.3 1.0 CG C:ASP69 4.8 47.4 1.0 CG C:ASP98 4.9 53.7 1.0 CE D:LYS254 4.9 49.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Maytansinoid-5C-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-5C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:77.2 occ:1.00 O D:HOH602 2.0 81.2 1.0 O D:HOH625 2.2 91.9 1.0 OE1 D:GLN11 2.3 98.6 1.0 O1A D:GDP501 2.3 97.3 1.0 O D:HOH621 2.5 76.8 1.0 O D:HOH613 2.9 77.3 1.0 CD D:GLN11 3.4 100.2 1.0 O D:HOH622 3.6 59.3 1.0 PA D:GDP501 3.7 71.0 1.0 NE2 D:GLN11 4.1 99.6 1.0 O2A D:GDP501 4.3 69.9 1.0 C5' D:GDP501 4.4 74.3 1.0 CB D:GLN11 4.4 97.2 1.0 OD1 D:ASN101 4.5 99.7 1.0 CG D:GLN11 4.5 99.1 1.0 O5' D:GDP501 4.6 72.1 1.0 O3A D:GDP501 4.8 83.3 1.0 O3B D:GDP501 4.8 77.7 1.0 O1B D:GDP501 4.8 82.3 1.0 ND2 D:ASN101 5.0 101.5 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Maytansinoid-5C-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-5C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:78.0 occ:1.00 OE2 F:GLU331 2.3 92.8 1.0 O1B F:ACP401 2.5 107.1 1.0 O1G F:ACP401 2.8 101.8 1.0 ND2 F:ASN333 3.1 103.3 1.0 CD F:GLU331 3.1 90.5 1.0 OE1 F:GLU331 3.3 95.5 1.0 OD1 F:ASN333 3.8 106.3 1.0 PB F:ACP401 3.8 117.5 1.0 CG F:ASN333 3.8 97.8 1.0 PG F:ACP401 3.8 112.7 1.0 O3G F:ACP401 3.8 90.3 1.0 NZ F:LYS74 4.0 89.0 1.0 O2B F:ACP401 4.1 107.8 1.0 C3B F:ACP401 4.4 110.4 1.0 CG F:GLU331 4.5 76.7 1.0 O1A F:ACP401 4.9 105.6 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