Magnesium in PDB 8b7a: Tubulin - Maytansinoid - 4 Complex

The structure of Tubulin - Maytansinoid - 4 Complex, PDB code: 8b7a 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, F.J.Diaz, M.O.Steinmetz, A.E.Prota, S.Piaraccini, D.Passarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.15 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.271, 158.55, 181.846, 90, 90, 90
R / Rfree (%)	18.1 / 22.3

The structure of Tubulin - Maytansinoid - 4 Complex also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Tubulin - Maytansinoid - 4 Complex (pdb code 8b7a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Tubulin - Maytansinoid - 4 Complex, PDB code: 8b7a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Tubulin - Maytansinoid - 4 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 - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.6 occ:1.00 O A:HOH603 2.0 43.3 1.0 O A:HOH689 2.0 42.7 1.0 O A:HOH650 2.1 44.1 1.0 O1G A:GTP501 2.1 38.5 1.0 O A:HOH623 2.1 47.9 1.0 O1B A:GTP501 2.3 31.6 1.0 OE1 A:GLU71 3.3 92.1 1.0 PG A:GTP501 3.3 49.2 1.0 PB A:GTP501 3.4 41.1 1.0 O3B A:GTP501 3.7 62.0 1.0 O3A A:GTP501 3.9 50.8 1.0 O2G A:GTP501 3.9 47.2 1.0 NZ B:LYS254 4.0 57.1 1.0 OD1 A:ASP69 4.1 50.8 1.0 CB A:GLN11 4.2 43.0 1.0 CD A:GLU71 4.2 82.0 1.0 OD2 A:ASP69 4.3 55.9 1.0 CB A:ASP98 4.3 45.5 1.0 OD2 A:ASP98 4.4 61.3 1.0 O A:HOH612 4.4 53.4 1.0 N A:GLN11 4.5 41.9 1.0 O3G A:GTP501 4.5 42.5 1.0 OE1 A:GLN11 4.6 55.8 1.0 CG A:ASP98 4.7 55.0 1.0 CG A:ASP69 4.7 57.6 1.0 OE2 A:GLU71 4.7 93.4 1.0 O2B A:GTP501 4.7 42.7 1.0 O1A A:GTP501 4.7 47.5 1.0 PA A:GTP501 4.8 46.6 1.0 CA A:GLN11 4.9 40.4 1.0

Magnesium binding site 2 out of 6 in the Tubulin - Maytansinoid - 4 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 - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:95.4 occ:1.00 O A:HOH717 3.5 70.9 1.0 O A:LYS164 3.8 78.3 1.0 OD2 A:ASP199 3.8 56.4 1.0 OD1 A:ASP199 3.9 60.3 1.0 O A:GLY162 4.0 78.0 1.0 CA E:CA201 4.2 112.2 1.0 CG A:ASP199 4.2 57.1 1.0 C A:LYS164 4.3 74.7 1.0 O A:LYS163 4.4 93.1 1.0 C A:LYS163 4.5 87.6 1.0 CA A:SER165 4.6 58.9 1.0 O A:HOH720 4.7 73.6 1.0 N A:SER165 4.7 57.4 1.0 N A:LYS164 4.8 76.1 1.0 OG A:SER165 4.9 63.8 1.0 CA A:LYS163 5.0 88.1 1.0

Magnesium binding site 3 out of 6 in the Tubulin - Maytansinoid - 4 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 - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:41.1 occ:1.00 O B:HOH663 2.0 39.4 1.0 O B:HOH707 2.1 51.7 1.0 OE1 B:GLN11 2.1 58.0 1.0 O C:HOH701 2.2 51.9 1.0 O1A B:GDP501 2.2 45.0 1.0 O B:HOH626 2.4 53.4 1.0 CD B:GLN11 3.3 61.0 1.0 O B:HOH649 3.4 60.5 1.0 OD2 B:ASP179 3.6 61.9 1.0 PA B:GDP501 3.6 36.0 1.0 O B:HOH773 4.0 65.7 1.0 O3A B:GDP501 4.1 42.2 1.0 CB B:GLN11 4.1 37.3 1.0 CG B:GLN11 4.2 48.4 1.0 NE2 B:GLN11 4.3 67.8 1.0 OD1 B:ASN101 4.3 46.8 1.0 C5' B:GDP501 4.3 44.4 1.0 O C:HOH619 4.3 54.8 1.0 O B:HOH759 4.4 76.1 1.0 O5' B:GDP501 4.5 33.4 1.0 O2A B:GDP501 4.7 37.8 1.0 O1B B:GDP501 4.7 40.5 1.0 CG B:ASP179 4.7 57.2 1.0 OE1 C:GLU254 4.7 56.2 1.0 O B:HOH766 4.8 79.5 1.0 C8 B:GDP501 4.8 49.0 1.0

Magnesium binding site 4 out of 6 in the Tubulin - Maytansinoid - 4 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 - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.0 occ:1.00 O C:HOH650 2.0 33.2 1.0 O C:HOH685 2.0 39.4 1.0 O C:HOH714 2.0 37.7 1.0 O1G C:GTP501 2.0 35.1 1.0 O1B C:GTP501 2.1 37.5 1.0 O C:HOH649 2.1 36.1 1.0 PG C:GTP501 3.2 40.8 1.0 PB C:GTP501 3.2 35.5 1.0 O3B C:GTP501 3.6 44.5 1.0 O2G C:GTP501 3.6 41.0 1.0 O3A C:GTP501 3.6 46.5 1.0 NZ D:LYS254 4.0 45.5 1.0 OD1 C:ASP69 4.0 43.5 1.0 OE2 C:GLU71 4.1 57.4 1.0 OD2 C:ASP69 4.1 41.7 1.0 OD2 C:ASP98 4.2 54.4 1.0 CB C:GLN11 4.2 29.0 1.0 CG C:GLU71 4.2 57.8 1.0 N C:GLN11 4.4 34.2 1.0 O3G C:GTP501 4.5 31.5 1.0 CB C:ASP98 4.5 41.0 1.0 CG C:ASP69 4.5 43.3 1.0 O2B C:GTP501 4.5 47.4 1.0 O C:HOH632 4.5 48.1 1.0 NE2 C:GLN11 4.6 53.2 1.0 O1A C:GTP501 4.7 43.6 1.0 CD C:GLU71 4.7 55.4 1.0 CG C:ASP98 4.7 47.2 1.0 PA C:GTP501 4.7 43.8 1.0 CA C:GLN11 4.9 38.1 1.0

Magnesium binding site 5 out of 6 in the Tubulin - Maytansinoid - 4 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 - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:76.0 occ:1.00 O D:HOH603 2.0 62.5 1.0 OE1 D:GLN11 2.3 84.9 1.0 O1A D:GDP501 2.4 95.9 1.0 O D:HOH646 3.1 65.4 1.0 O D:HOH689 3.3 73.3 1.0 CD D:GLN11 3.3 92.5 1.0 PA D:GDP501 3.8 67.9 1.0 NE2 D:GLN11 3.9 96.9 1.0 O2A D:GDP501 4.2 61.2 1.0 C5' D:GDP501 4.3 63.4 1.0 CG D:GLN11 4.4 89.2 1.0 CB D:GLN11 4.4 88.1 1.0 O5' D:GDP501 4.5 64.1 1.0 C8 D:GDP501 4.7 57.6 1.0 OD1 D:ASN101 4.9 84.9 1.0 O1B D:GDP501 5.0 57.6 1.0 O3A D:GDP501 5.0 74.6 1.0

Magnesium binding site 6 out of 6 in the Tubulin - Maytansinoid - 4 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tubulin - Maytansinoid - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:95.8 occ:1.00 OE2 F:GLU331 2.3 108.8 1.0 O3G F:ACP401 2.5 119.7 1.0 O1B F:ACP401 2.6 121.4 1.0 ND2 F:ASN333 3.2 100.3 1.0 CD F:GLU331 3.3 103.4 1.0 OE1 F:GLU331 3.6 111.4 1.0 PG F:ACP401 3.7 124.5 1.0 PB F:ACP401 3.7 125.4 1.0 C3B F:ACP401 3.9 127.9 1.0 CG F:ASN333 4.2 93.3 1.0 O2G F:ACP401 4.2 109.4 1.0 O2B F:ACP401 4.3 128.9 1.0 NZ F:LYS74 4.4 90.9 1.0 OD1 F:ASN333 4.5 101.7 1.0 CG F:GLU331 4.6 91.7 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