Magnesium in PDB 5sb8: Tubulin-Maytansinoid-3-Complex

The structure of Tubulin-Maytansinoid-3-Complex, PDB code: 5sb8 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)	49.66 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.664, 157.491, 181.511, 90, 90, 90
R / Rfree (%)	19.3 / 23

The structure of Tubulin-Maytansinoid-3-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-3-Complex (pdb code 5sb8). 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-3-Complex, PDB code: 5sb8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Maytansinoid-3-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-3-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:38.0 occ:1.00 O A:HOH603 2.0 40.5 1.0 O A:HOH648 2.0 43.5 1.0 O1G A:GTP501 2.1 35.5 1.0 O A:HOH642 2.1 42.0 1.0 O1B A:GTP501 2.1 35.4 1.0 O A:HOH607 2.2 40.1 1.0 PB A:GTP501 3.2 39.2 1.0 PG A:GTP501 3.3 45.4 1.0 O3B A:GTP501 3.6 56.8 1.0 O3A A:GTP501 3.7 51.6 1.0 OE1 A:GLU71 3.7 81.4 1.0 O2G A:GTP501 3.9 43.7 1.0 NZ B:LYS254 4.0 48.9 1.0 CB A:GLN11 4.1 45.7 1.0 OD1 A:ASP69 4.1 49.6 1.0 OD2 A:ASP69 4.3 54.4 1.0 CD A:GLU71 4.4 66.3 1.0 N A:GLN11 4.4 45.0 1.0 OE2 A:GLU71 4.5 67.6 1.0 NE2 A:GLN11 4.5 51.8 1.0 O3G A:GTP501 4.5 42.2 1.0 O2B A:GTP501 4.5 45.4 1.0 O1A A:GTP501 4.6 43.2 1.0 CB A:ASP98 4.6 44.8 1.0 OD2 A:ASP98 4.6 55.4 1.0 PA A:GTP501 4.7 42.6 1.0 CG A:ASP69 4.7 55.5 1.0 CA A:GLN11 4.8 45.6 1.0 CG A:ASP98 4.9 50.8 1.0 O B:HOH610 4.9 45.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Maytansinoid-3-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-3-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:35.8 occ:1.00 O B:HOH640 2.0 45.6 1.0 O C:HOH662 2.2 47.2 1.0 OE1 B:GLN11 2.3 45.1 1.0 O1A B:GDP501 2.3 46.4 1.0 O B:HOH628 2.3 55.0 1.0 O B:HOH669 2.4 46.0 1.0 CD B:GLN11 3.5 55.3 1.0 PA B:GDP501 3.7 37.6 1.0 OD2 B:ASP179 3.8 44.9 1.0 O C:HOH775 3.8 63.2 1.0 O3A B:GDP501 4.1 43.0 1.0 OD1 B:ASN101 4.2 44.6 1.0 CB B:GLN11 4.3 37.4 1.0 C5' B:GDP501 4.4 41.6 1.0 NE2 B:GLN11 4.4 49.0 1.0 CG B:GLN11 4.4 45.9 1.0 O5' B:GDP501 4.5 37.5 1.0 OE1 C:GLU254 4.6 47.9 1.0 O1B B:GDP501 4.7 38.3 1.0 CG B:ASP179 4.7 47.6 1.0 O2A B:GDP501 4.8 38.7 1.0 C8 B:GDP501 4.9 44.3 1.0 ND2 B:ASN101 5.0 41.6 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Maytansinoid-3-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-3-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:35.8 occ:1.00 O C:HOH677 2.0 40.1 1.0 O C:HOH626 2.0 35.7 1.0 O C:HOH652 2.0 37.3 1.0 O1G C:GTP501 2.0 37.0 1.0 O1B C:GTP501 2.1 33.7 1.0 O C:HOH674 2.1 40.7 1.0 PG C:GTP501 3.2 39.6 1.0 PB C:GTP501 3.2 31.9 1.0 O3B C:GTP501 3.5 43.3 1.0 O3A C:GTP501 3.6 43.5 1.0 O2G C:GTP501 3.7 39.5 1.0 NZ D:LYS254 4.0 47.0 1.0 OD1 C:ASP69 4.0 37.9 1.0 OE2 C:GLU71 4.1 52.1 1.0 OD2 C:ASP69 4.1 38.9 1.0 CB C:GLN11 4.2 37.4 1.0 CG C:GLU71 4.3 48.7 1.0 OD2 C:ASP98 4.3 47.2 1.0 N C:GLN11 4.4 36.0 1.0 O3G C:GTP501 4.4 35.3 1.0 CB C:ASP98 4.4 41.5 1.0 O C:HOH661 4.5 48.6 1.0 O2B C:GTP501 4.5 37.3 1.0 CG C:ASP69 4.5 41.8 1.0 NE2 C:GLN11 4.6 49.0 1.0 CD C:GLU71 4.7 47.6 1.0 O1A C:GTP501 4.7 39.2 1.0 PA C:GTP501 4.7 37.1 1.0 CG C:ASP98 4.8 44.0 1.0 CA C:GLN11 4.9 36.5 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Maytansinoid-3-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-3-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:77.5 occ:1.00 O1A D:GDP501 2.1 96.5 1.0 OE1 D:GLN11 2.9 87.9 1.0 O D:HOH611 3.2 76.5 1.0 CD D:GLN11 3.4 91.5 1.0 PA D:GDP501 3.5 66.1 1.0 NE2 D:GLN11 3.7 97.9 1.0 O D:HOH626 3.8 72.9 1.0 C5' D:GDP501 4.0 73.2 1.0 OD1 D:ASN101 4.2 97.7 1.0 O5' D:GDP501 4.3 68.4 1.0 O2A D:GDP501 4.3 63.0 1.0 O1B D:GDP501 4.3 71.9 1.0 CB D:GLN11 4.5 81.2 1.0 CG D:GLN11 4.5 88.3 1.0 O3A D:GDP501 4.5 70.9 1.0 ND2 D:ASN101 4.7 107.6 1.0 CG D:ASN101 4.9 97.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Maytansinoid-3-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-3-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:92.9 occ:1.00 OE2 F:GLU331 2.5 96.8 1.0 O1B F:ACP401 2.6 107.1 1.0 O3G F:ACP401 2.7 91.2 1.0 ND2 F:ASN333 2.8 95.3 1.0 CD F:GLU331 3.3 91.1 1.0 OE1 F:GLU331 3.3 95.6 1.0 CG F:ASN333 4.0 92.1 1.0 NZ F:LYS74 4.0 90.5 1.0 PB F:ACP401 4.1 112.6 1.0 PG F:ACP401 4.1 116.5 1.0 OD1 F:ASN333 4.4 96.5 1.0 O2G F:ACP401 4.5 93.6 1.0 O2B F:ACP401 4.7 111.0 1.0 CG F:GLU331 4.7 78.4 1.0 C3B F:ACP401 4.8 103.4 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