Magnesium in PDB 8b7c: Tubulin-Maytansinoid-12 Complex

The structure of Tubulin-Maytansinoid-12 Complex, PDB code: 8b7c was solved by Z.Boiarska, H.Perez-Pena, A.-C.Abel, P.Marzullo, B.Alvarez-Bernad, F.Bonato, B.Santini, D.Horvath, D.Lucena-Agell, F.Vasile, M.Sironi, J.F.Diaz, M.O.Steinmetz, A.E.Prota, S.Pieraccini, D.Passarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.57 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.866, 157.939, 180.57, 90, 90, 90
R / Rfree (%)	18.3 / 21.2

The structure of Tubulin-Maytansinoid-12 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-12 Complex (pdb code 8b7c). 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-12 Complex, PDB code: 8b7c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Maytansinoid-12 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-12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:34.0 occ:1.00 O A:HOH640 2.0 31.7 1.0 O A:HOH729 2.1 31.1 1.0 O1G A:GTP501 2.1 29.5 1.0 O A:HOH614 2.1 35.8 1.0 O A:HOH645 2.1 32.9 1.0 O1B A:GTP501 2.1 27.9 1.0 PG A:GTP501 3.2 34.4 1.0 PB A:GTP501 3.3 31.5 1.0 O3B A:GTP501 3.6 38.6 1.0 O2G A:GTP501 3.7 33.5 1.0 OE1 A:GLU71 3.7 68.5 1.0 O3A A:GTP501 3.8 36.9 1.0 NZ B:LYS254 3.8 39.0 1.0 OD1 A:ASP69 4.0 37.2 1.0 CB A:GLN11 4.2 30.9 1.0 OD2 A:ASP69 4.2 40.4 1.0 OD2 A:ASP98 4.3 41.3 1.0 CB A:ASP98 4.4 35.6 1.0 N A:GLN11 4.4 29.9 1.0 O A:HOH710 4.4 54.0 1.0 O3G A:GTP501 4.5 31.2 1.0 O2B A:GTP501 4.6 35.9 1.0 CG A:ASP69 4.6 41.8 1.0 O1A A:GTP501 4.6 31.2 1.0 CG A:ASP98 4.7 41.0 1.0 PA A:GTP501 4.8 33.1 1.0 CA A:GLN11 4.9 32.1 1.0 OE1 A:GLN11 4.9 43.8 1.0 CD A:GLU71 4.9 76.8 1.0 CE B:LYS254 4.9 37.5 1.0 CB A:GLU71 5.0 70.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Maytansinoid-12 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-12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:26.5 occ:1.00 O B:HOH699 2.0 35.2 1.0 O B:HOH730 2.1 54.4 1.0 OE1 B:GLN11 2.2 42.8 1.0 O1A B:GDP501 2.3 31.9 1.0 O C:HOH662 2.3 49.0 1.0 O B:HOH622 2.4 41.5 1.0 CD B:GLN11 3.4 48.4 1.0 O B:HOH820 3.5 68.1 1.0 PA B:GDP501 3.6 31.9 1.0 OD2 B:ASP179 3.9 39.2 1.0 O3A B:GDP501 3.9 33.8 1.0 O B:HOH614 4.1 84.7 1.0 CB B:GLN11 4.1 33.2 1.0 CG B:GLN11 4.2 40.7 1.0 O B:HOH799 4.3 67.7 1.0 C5' B:GDP501 4.3 32.3 1.0 NE2 B:GLN11 4.4 52.2 1.0 O5' B:GDP501 4.4 33.0 1.0 OD1 B:ASN101 4.4 36.6 1.0 O C:HOH637 4.5 55.9 1.0 OE1 C:GLU254 4.6 39.3 1.0 O1B B:GDP501 4.7 27.1 1.0 O2A B:GDP501 4.7 30.8 1.0 CG B:ASP179 4.8 40.9 1.0 O B:HOH768 4.8 69.1 1.0 C8 B:GDP501 4.8 39.2 1.0 PB B:GDP501 4.9 31.8 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Maytansinoid-12 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-12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:29.7 occ:1.00 O C:HOH760 2.0 28.3 1.0 O C:HOH636 2.0 29.3 1.0 O1G C:GTP501 2.0 27.5 1.0 O C:HOH668 2.1 28.6 1.0 O1B C:GTP501 2.1 28.9 1.0 O C:HOH724 2.2 30.3 1.0 PG C:GTP501 3.2 32.0 1.0 PB C:GTP501 3.3 30.1 1.0 O3B C:GTP501 3.6 33.0 1.0 O2G C:GTP501 3.7 32.9 1.0 O3A C:GTP501 3.8 33.6 1.0 OE2 C:GLU71 3.9 48.3 1.0 NZ D:LYS254 3.9 34.0 1.0 OD1 C:ASP69 4.1 32.4 1.0 CG C:GLU71 4.1 42.8 1.0 OD2 C:ASP69 4.1 33.2 1.0 CB C:GLN11 4.2 27.6 1.0 OD2 C:ASP98 4.3 43.9 1.0 CB C:ASP98 4.4 33.0 1.0 N C:GLN11 4.4 25.9 1.0 CD C:GLU71 4.5 48.2 1.0 O3G C:GTP501 4.5 29.9 1.0 O2B C:GTP501 4.5 31.4 1.0 CG C:ASP69 4.5 32.7 1.0 O1A C:GTP501 4.6 30.4 1.0 O C:HOH634 4.6 45.5 1.0 CG C:ASP98 4.7 38.1 1.0 PA C:GTP501 4.8 30.6 1.0 NE2 C:GLN11 4.9 34.9 1.0 CA C:GLN11 4.9 27.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Maytansinoid-12 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-12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:61.2 occ:1.00 O D:HOH618 2.0 54.3 1.0 O1A D:GDP501 2.2 68.1 1.0 OE1 D:GLN11 2.2 77.6 1.0 O D:HOH645 3.1 50.8 1.0 CD D:GLN11 3.3 75.0 1.0 PA D:GDP501 3.7 58.3 1.0 NE2 D:GLN11 4.2 72.6 1.0 CB D:GLN11 4.2 55.2 1.0 CG D:GLN11 4.2 66.9 1.0 C5' D:GDP501 4.3 56.8 1.0 O D:HOH718 4.4 62.4 1.0 O3A D:GDP501 4.5 51.3 1.0 O5' D:GDP501 4.5 58.0 1.0 O2A D:GDP501 4.5 58.1 1.0 O1B D:GDP501 4.7 44.8 1.0 C8 D:GDP501 4.9 44.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Maytansinoid-12 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-12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:69.4 occ:1.00 OE2 F:GLU331 2.0 101.7 1.0 O3G F:ACP401 2.1 80.0 1.0 O1B F:ACP401 2.5 99.7 1.0 ND2 F:ASN333 3.0 100.1 1.0 CD F:GLU331 3.2 90.7 1.0 PG F:ACP401 3.3 98.4 1.0 PB F:ACP401 3.7 93.9 1.0 C3B F:ACP401 3.7 96.2 1.0 NZ F:LYS74 3.7 79.9 1.0 O2G F:ACP401 3.8 94.6 1.0 CG F:ASN333 4.0 91.9 1.0 CG F:GLU331 4.0 78.8 1.0 OE1 F:GLU331 4.1 97.2 1.0 OD1 F:ASN333 4.2 99.9 1.0 O2B F:ACP401 4.5 99.8 1.0 O1G F:ACP401 4.7 93.9 1.0 O3A F:ACP401 4.9 90.3 1.0

Z.Boiarska, H.Perez-Pena, A.C.Abel, P.Marzullo, B.Alvarez-Bernad, F.Bonato, B.Santini, D.Horvath, D.Lucena-Agell, F.Vasile, M.Sironi, J.F.Diaz, A.E.Prota, S.Pieraccini, D.Passarella. Maytansinol Functionalization: Towards Useful Probes For Studying Microtubule Dynamics. Chemistry V. 29 03431 2023.
ISSN: ISSN 0947-6539
PubMed: 36468686
DOI: 10.1002/CHEM.202203431