Magnesium in PDB 5sbc: Tubulin-Maytansinoid-5A-Complex

The structure of Tubulin-Maytansinoid-5A-Complex, PDB code: 5sbc 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)	48.02 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.911, 157.908, 181.461, 90, 90, 90
R / Rfree (%)	18.6 / 22.8

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

Magnesium binding site 1 out of 5 in the Tubulin-Maytansinoid-5A-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-5A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:42.0 occ:1.00 O A:HOH607 2.0 37.7 1.0 O1G A:GTP501 2.0 32.7 1.0 O1B A:GTP501 2.1 33.5 1.0 O A:HOH676 2.1 44.5 1.0 O A:HOH620 2.2 43.1 1.0 O A:HOH633 2.2 42.5 1.0 PG A:GTP501 3.2 45.5 1.0 PB A:GTP501 3.2 36.4 1.0 O3B A:GTP501 3.5 58.0 1.0 OE1 A:GLU71 3.5 73.9 1.0 O3A A:GTP501 3.8 52.0 1.0 O2G A:GTP501 3.8 41.9 1.0 OD1 A:ASP69 4.0 48.0 1.0 CB A:GLN11 4.1 43.3 1.0 NZ B:LYS254 4.1 51.4 1.0 OD2 A:ASP69 4.2 55.3 1.0 N A:GLN11 4.3 42.5 1.0 CB A:ASP98 4.4 46.9 1.0 O3G A:GTP501 4.4 40.6 1.0 O2B A:GTP501 4.5 50.9 1.0 OD2 A:ASP98 4.5 53.3 1.0 NE2 A:GLN11 4.5 47.2 1.0 CG A:ASP69 4.6 54.9 1.0 O1A A:GTP501 4.6 38.7 1.0 CG A:ASP98 4.7 48.1 1.0 CD A:GLU71 4.7 70.2 1.0 PA A:GTP501 4.7 41.9 1.0 CA A:GLN11 4.8 43.5 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Maytansinoid-5A-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-5A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:34.0 occ:1.00 O B:HOH646 2.0 36.2 1.0 OE1 B:GLN11 2.2 51.3 1.0 O B:HOH602 2.2 53.5 1.0 O C:HOH760 2.2 45.7 1.0 O1A B:GDP501 2.3 41.0 1.0 O B:HOH709 2.4 43.9 1.0 CD B:GLN11 3.4 57.0 1.0 PA B:GDP501 3.6 33.5 1.0 OD2 B:ASP179 3.8 43.0 1.0 O3A B:GDP501 3.9 37.2 1.0 OD1 B:ASN101 4.1 45.7 1.0 CB B:GLN11 4.1 39.0 1.0 NE2 B:GLN11 4.3 61.4 1.0 CG B:GLN11 4.3 52.7 1.0 C5' B:GDP501 4.4 42.7 1.0 O1B B:GDP501 4.4 33.8 1.0 O5' B:GDP501 4.4 34.0 1.0 O C:HOH627 4.6 64.2 1.0 O2A B:GDP501 4.7 37.7 1.0 OE1 C:GLU254 4.7 49.2 1.0 PB B:GDP501 4.8 36.2 1.0 CG B:ASP179 4.8 43.1 1.0 ND2 B:ASN101 4.9 40.9 1.0 CG B:ASN101 4.9 39.8 1.0 C8 B:GDP501 5.0 44.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Maytansinoid-5A-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-5A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:38.3 occ:1.00 O1G C:GTP501 1.9 37.3 1.0 O C:HOH641 2.0 34.1 1.0 O C:HOH723 2.1 41.0 1.0 O C:HOH658 2.1 30.0 1.0 O1B C:GTP501 2.1 33.5 1.0 O C:HOH652 2.1 41.5 1.0 PG C:GTP501 3.1 37.0 1.0 PB C:GTP501 3.2 35.1 1.0 O3B C:GTP501 3.5 41.7 1.0 O3A C:GTP501 3.6 49.7 1.0 O2G C:GTP501 3.6 37.6 1.0 NZ D:LYS254 3.9 46.8 1.0 OE2 C:GLU71 4.0 50.8 1.0 OD1 C:ASP69 4.2 37.9 1.0 OD2 C:ASP98 4.2 47.1 1.0 CB C:GLN11 4.3 37.6 1.0 O3G C:GTP501 4.3 36.2 1.0 OD2 C:ASP69 4.3 38.7 1.0 CG C:GLU71 4.3 46.1 1.0 CB C:ASP98 4.3 41.1 1.0 O2B C:GTP501 4.5 46.3 1.0 N C:GLN11 4.5 36.2 1.0 O C:HOH620 4.6 68.4 1.0 CG C:ASP98 4.7 44.7 1.0 CD C:GLU71 4.7 48.9 1.0 CG C:ASP69 4.7 39.6 1.0 PA C:GTP501 4.7 38.1 1.0 O1A C:GTP501 4.7 40.8 1.0 OE1 C:GLN11 4.8 59.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Maytansinoid-5A-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-5A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:65.5 occ:1.00 O D:HOH622 2.1 66.1 1.0 O1A D:GDP501 2.2 93.8 1.0 OE1 D:GLN11 2.4 85.4 1.0 O D:HOH675 3.1 66.2 1.0 O D:HOH637 3.3 82.4 1.0 CD D:GLN11 3.6 98.6 1.0 PA D:GDP501 3.7 69.6 1.0 C5' D:GDP501 4.1 69.3 1.0 O5' D:GDP501 4.4 73.4 1.0 O1B D:GDP501 4.4 101.4 1.0 NE2 D:GLN11 4.5 90.0 1.0 O3A D:GDP501 4.5 60.0 1.0 O2A D:GDP501 4.5 63.0 1.0 CB D:GLN11 4.5 96.2 1.0 CG D:GLN11 4.6 90.0 1.0 OD1 D:ASN101 4.7 94.2 1.0 C8 D:GDP501 4.9 63.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Maytansinoid-5A-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-5A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:86.0 occ:1.00 O1B F:ACP401 2.4 106.3 1.0 O3G F:ACP401 2.6 105.6 1.0 OE2 F:GLU331 2.7 105.9 1.0 ND2 F:ASN333 2.7 97.4 1.0 CD F:GLU331 3.4 93.0 1.0 OE1 F:GLU331 3.4 103.3 1.0 PB F:ACP401 3.8 107.0 1.0 PG F:ACP401 3.9 124.7 1.0 CG F:ASN333 4.0 101.5 1.0 NZ F:LYS74 4.0 97.9 1.0 O2B F:ACP401 4.3 113.9 1.0 O2G F:ACP401 4.4 97.0 1.0 OD1 F:ASN333 4.5 103.2 1.0 C3B F:ACP401 4.6 106.4 1.0 CG F:GLU331 4.8 80.0 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