Magnesium in PDB 8b7b: Tubulin - Maytansinoid - 6 Complex

The structure of Tubulin - Maytansinoid - 6 Complex, PDB code: 8b7b 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)	47.83 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.085, 155.637, 181.924, 90, 90, 90
R / Rfree (%)	18.4 / 22.4

The structure of Tubulin - Maytansinoid - 6 Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	5 atoms

The binding sites of Magnesium atom in the Tubulin - Maytansinoid - 6 Complex (pdb code 8b7b). 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 - 6 Complex, PDB code: 8b7b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin - Maytansinoid - 6 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 - 6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:42.5 occ:1.00 O1G A:GTP501 2.0 38.0 1.0 O A:HOH643 2.0 42.5 1.0 O A:HOH661 2.0 40.9 1.0 O1B A:GTP501 2.1 36.3 1.0 O A:HOH619 2.2 40.5 1.0 O A:HOH614 2.3 45.0 1.0 PG A:GTP501 3.2 44.5 1.0 PB A:GTP501 3.2 40.5 1.0 O3B A:GTP501 3.5 55.2 1.0 O2G A:GTP501 3.7 44.1 1.0 O3A A:GTP501 3.8 55.2 1.0 OE1 A:GLU71 3.9 69.7 1.0 OD1 A:ASP69 3.9 51.5 1.0 NZ B:LYS254 4.0 52.8 1.0 CB A:GLN11 4.1 47.0 1.0 OD2 A:ASP69 4.2 58.4 1.0 N A:GLN11 4.3 47.1 1.0 OD2 A:ASP98 4.3 51.8 1.0 O3G A:GTP501 4.4 38.6 1.0 CB A:ASP98 4.4 49.7 1.0 O A:HOH618 4.5 57.5 1.0 CG A:ASP69 4.5 59.7 1.0 O2B A:GTP501 4.5 44.2 1.0 O1A A:GTP501 4.5 46.6 1.0 CG A:ASP98 4.7 51.6 1.0 NE2 A:GLN11 4.7 49.2 1.0 PA A:GTP501 4.7 44.8 1.0 CA A:GLN11 4.8 46.8 1.0 CB A:GLU71 4.9 69.5 1.0 CD A:GLU71 5.0 84.0 1.0

Magnesium binding site 2 out of 5 in the Tubulin - Maytansinoid - 6 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 - 6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:41.3 occ:1.00 O B:HOH640 2.0 42.3 1.0 O B:HOH710 2.1 55.9 1.0 O1A B:GDP501 2.2 43.9 1.0 OE1 B:GLN11 2.4 51.4 1.0 O C:HOH681 2.4 56.6 1.0 O B:HOH615 2.6 53.8 1.0 O B:HOH707 3.4 59.2 1.0 PA B:GDP501 3.6 39.7 1.0 O B:HOH769 3.6 65.8 1.0 CD B:GLN11 3.6 50.3 1.0 OD2 B:ASP179 3.6 51.0 1.0 O3A B:GDP501 4.0 47.1 1.0 OD1 B:ASN101 4.0 46.5 1.0 CB B:GLN11 4.3 42.9 1.0 C5' B:GDP501 4.3 45.8 1.0 CG B:GLN11 4.4 45.5 1.0 O5' B:GDP501 4.4 43.6 1.0 O C:HOH610 4.5 63.8 1.0 NE2 B:GLN11 4.6 54.2 1.0 O2A B:GDP501 4.6 36.8 1.0 OE1 C:GLU254 4.6 54.8 1.0 O1B B:GDP501 4.7 36.7 1.0 CG B:ASP179 4.7 58.4 1.0 C8 B:GDP501 4.8 42.3 1.0 O B:HOH730 4.8 67.5 1.0 ND2 B:ASN101 4.9 45.4 1.0 CG B:ASN101 4.9 50.1 1.0 PB B:GDP501 5.0 37.2 1.0

Magnesium binding site 3 out of 5 in the Tubulin - Maytansinoid - 6 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 - 6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:40.2 occ:1.00 O C:HOH694 1.9 41.4 1.0 O C:HOH630 2.0 38.7 1.0 O1G C:GTP501 2.1 32.2 1.0 O C:HOH660 2.1 41.0 1.0 O C:HOH638 2.1 44.2 1.0 O1B C:GTP501 2.2 36.2 1.0 PG C:GTP501 3.2 41.4 1.0 PB C:GTP501 3.2 35.7 1.0 O3B C:GTP501 3.6 49.7 1.0 O3A C:GTP501 3.7 52.4 1.0 O2G C:GTP501 3.7 39.8 1.0 OE2 C:GLU71 3.9 51.4 1.0 NZ D:LYS254 3.9 49.6 1.0 OD1 C:ASP69 4.1 44.7 1.0 CB C:GLN11 4.2 38.6 1.0 OD2 C:ASP98 4.2 48.5 1.0 OD2 C:ASP69 4.2 39.7 1.0 CG C:GLU71 4.2 50.7 1.0 N C:GLN11 4.4 37.4 1.0 CB C:ASP98 4.5 42.4 1.0 O3G C:GTP501 4.5 37.7 1.0 O2B C:GTP501 4.6 46.3 1.0 CD C:GLU71 4.6 48.3 1.0 CG C:ASP69 4.6 47.7 1.0 O1A C:GTP501 4.6 38.8 1.0 O C:HOH693 4.7 74.5 1.0 NE2 C:GLN11 4.7 46.6 1.0 PA C:GTP501 4.7 42.4 1.0 CG C:ASP98 4.7 46.2 1.0 CA C:GLN11 4.9 37.9 1.0

Magnesium binding site 4 out of 5 in the Tubulin - Maytansinoid - 6 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 - 6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:65.9 occ:1.00 O D:HOH605 2.0 77.0 1.0 O D:HOH646 2.0 79.8 1.0 OE1 D:GLN11 2.1 79.7 1.0 O1A D:GDP501 2.5 108.6 1.0 O D:HOH618 2.6 67.9 1.0 CD D:GLN11 3.3 86.4 1.0 PA D:GDP501 3.6 73.3 1.0 O2A D:GDP501 3.6 67.9 1.0 NE2 D:GLN11 4.1 86.7 1.0 C5' D:GDP501 4.2 77.7 1.0 CG D:GLN11 4.3 89.6 1.0 CB D:GLN11 4.3 75.1 1.0 O D:HOH608 4.4 79.8 1.0 O5' D:GDP501 4.4 71.0 1.0 OD1 D:ASN101 4.5 114.6 1.0 O1B D:GDP501 4.6 69.3 1.0 O3A D:GDP501 4.9 89.0 1.0 ND2 D:ASN101 4.9 122.8 1.0 C8 D:GDP501 5.0 67.6 1.0

Magnesium binding site 5 out of 5 in the Tubulin - Maytansinoid - 6 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 - 6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:92.3 occ:1.00 O3G F:ACP401 1.9 85.2 1.0 OE2 F:GLU331 2.4 111.2 1.0 O1B F:ACP401 2.5 103.5 1.0 ND2 F:ASN333 3.0 102.6 1.0 CD F:GLU331 3.1 97.0 1.0 OE1 F:GLU331 3.2 101.8 1.0 PG F:ACP401 3.2 118.8 1.0 C3B F:ACP401 3.5 90.1 1.0 PB F:ACP401 3.5 110.5 1.0 NZ F:LYS74 3.9 102.9 1.0 O2G F:ACP401 4.0 100.6 1.0 CG F:ASN333 4.1 98.5 1.0 O2B F:ACP401 4.3 111.8 1.0 O1G F:ACP401 4.4 106.9 1.0 OD1 F:ASN333 4.5 102.9 1.0 CG F:GLU331 4.6 86.0 1.0 O3A F:ACP401 4.9 112.9 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