Magnesium in PDB 5sba: Tubulin-Maytansinoid-4B-Complex

The structure of Tubulin-Maytansinoid-4B-Complex, PDB code: 5sba 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)	49.49 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.174, 156.45, 180.827, 90, 90, 90
R / Rfree (%)	18.4 / 22.7

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

Magnesium binding site 1 out of 5 in the Tubulin-Maytansinoid-4B-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-4B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.5 occ:1.00 O1G A:GTP501 1.9 33.2 1.0 O A:HOH685 2.0 43.3 1.0 O A:HOH658 2.1 38.3 1.0 O A:HOH620 2.1 36.1 1.0 O A:HOH638 2.2 43.8 1.0 O1B A:GTP501 2.2 36.0 1.0 PG A:GTP501 3.1 36.8 1.0 PB A:GTP501 3.2 34.4 1.0 O3B A:GTP501 3.5 55.2 1.0 O3A A:GTP501 3.7 47.3 1.0 O2G A:GTP501 3.7 41.6 1.0 NZ B:LYS254 3.8 48.2 1.0 OE1 A:GLU71 3.9 57.1 1.0 OD1 A:ASP69 4.2 44.5 1.0 CB A:GLN11 4.3 36.8 1.0 OD2 A:ASP98 4.3 44.0 1.0 O3G A:GTP501 4.3 35.7 1.0 CB A:ASP98 4.3 40.7 1.0 N A:GLN11 4.5 44.0 1.0 CG A:ASP98 4.5 47.6 1.0 OD2 A:ASP69 4.6 46.0 1.0 O2B A:GTP501 4.6 44.4 1.0 O1A A:GTP501 4.7 39.2 1.0 OE1 A:GLN11 4.7 54.2 1.0 PA A:GTP501 4.7 37.1 1.0 CE B:LYS254 4.9 44.8 1.0 CG A:ASP69 4.9 45.5 1.0 CB A:GLU71 4.9 68.0 1.0 O B:HOH664 5.0 43.0 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Maytansinoid-4B-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-4B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:29.9 occ:1.00 O B:HOH671 1.9 42.4 1.0 OE1 B:GLN11 2.1 44.1 1.0 O1A B:GDP501 2.2 42.4 1.0 O C:HOH604 2.2 51.2 1.0 O B:HOH680 2.3 41.6 1.0 O B:HOH602 2.7 43.0 1.0 O C:HOH818 3.0 53.6 1.0 CD B:GLN11 3.4 50.2 1.0 PA B:GDP501 3.6 34.8 1.0 OD2 B:ASP179 3.8 47.6 1.0 CB B:GLN11 4.1 38.4 1.0 OE2 C:GLU254 4.1 49.0 1.0 O3A B:GDP501 4.1 40.5 1.0 CG B:GLN11 4.2 42.1 1.0 NE2 B:GLN11 4.3 49.2 1.0 OD1 B:ASN101 4.4 39.2 1.0 C5' B:GDP501 4.4 37.4 1.0 O C:HOH802 4.5 56.7 1.0 O5' B:GDP501 4.5 41.7 1.0 O2A B:GDP501 4.5 35.6 1.0 O1B B:GDP501 4.6 32.8 1.0 C8 B:GDP501 4.8 40.6 1.0 CG B:ASP179 4.9 49.3 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Maytansinoid-4B-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-4B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:35.8 occ:1.00 O C:HOH674 2.0 35.2 1.0 O1G C:GTP501 2.0 28.4 1.0 O C:HOH668 2.0 38.0 1.0 O C:HOH730 2.1 36.1 1.0 O1B C:GTP501 2.1 33.9 1.0 O C:HOH710 2.2 38.5 1.0 PG C:GTP501 3.2 33.4 1.0 PB C:GTP501 3.2 33.7 1.0 O3B C:GTP501 3.6 41.1 1.0 O2G C:GTP501 3.7 36.6 1.0 O3A C:GTP501 3.7 43.7 1.0 NZ D:LYS254 4.0 41.9 1.0 OD1 C:ASP69 4.0 34.5 1.0 OE2 C:GLU71 4.1 53.1 1.0 CG C:GLU71 4.2 40.3 1.0 CB C:GLN11 4.3 34.2 1.0 OD2 C:ASP69 4.3 35.0 1.0 CB C:ASP98 4.3 37.7 1.0 O3G C:GTP501 4.4 32.1 1.0 OD2 C:ASP98 4.4 43.0 1.0 N C:GLN11 4.4 32.9 1.0 O2B C:GTP501 4.5 33.5 1.0 CG C:ASP69 4.6 34.7 1.0 CD C:GLU71 4.7 44.8 1.0 NE2 C:GLN11 4.7 46.0 1.0 O1A C:GTP501 4.8 36.1 1.0 CG C:ASP98 4.8 39.4 1.0 PA C:GTP501 4.8 34.7 1.0 CA C:GLN11 5.0 33.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Maytansinoid-4B-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-4B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:68.2 occ:1.00 O D:HOH603 2.1 61.9 1.0 OE1 D:GLN11 2.3 70.4 1.0 O1A D:GDP501 2.4 91.7 1.0 O D:HOH716 2.7 60.7 1.0 O D:HOH670 3.2 71.1 1.0 CD D:GLN11 3.5 82.5 1.0 PA D:GDP501 3.8 62.9 1.0 O2A D:GDP501 4.3 60.3 1.0 C5' D:GDP501 4.3 68.8 1.0 NE2 D:GLN11 4.4 68.7 1.0 CB D:GLN11 4.4 68.3 1.0 CG D:GLN11 4.5 80.5 1.0 O5' D:GDP501 4.6 64.8 1.0 C8 D:GDP501 4.7 51.0 1.0 O1B D:GDP501 4.8 60.8 1.0 O3A D:GDP501 4.9 61.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Maytansinoid-4B-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-4B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:89.9 occ:1.00 OE2 F:GLU331 2.4 90.8 1.0 O3G F:ACP401 2.4 101.3 1.0 O1B F:ACP401 2.5 109.1 1.0 OD1 F:ASN333 2.9 95.5 1.0 CD F:GLU331 3.3 88.4 1.0 OE1 F:GLU331 3.4 95.7 1.0 NZ F:LYS74 3.7 93.0 1.0 PG F:ACP401 3.8 122.9 1.0 PB F:ACP401 3.9 109.8 1.0 CG F:ASN333 3.9 88.4 1.0 O2G F:ACP401 4.1 99.1 1.0 ND2 F:ASN333 4.4 84.6 1.0 O2B F:ACP401 4.4 114.7 1.0 C3B F:ACP401 4.5 102.3 1.0 O F:HOH541 4.6 74.5 1.0 CG F:GLU331 4.7 70.3 1.0 CE F:LYS74 4.9 95.1 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