Magnesium in PDB 7e4z: Crystal Structure of Tubulin in Complex with Maytansinol

The structure of Crystal Structure of Tubulin in Complex with Maytansinol, PDB code: 7e4z was solved by Y.Wang, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.29 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.431, 156.635, 182.275, 90, 90, 90
R / Rfree (%)	19.2 / 22.8

The structure of Crystal Structure of Tubulin in Complex with Maytansinol also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Tubulin in Complex with Maytansinol (pdb code 7e4z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Tubulin in Complex with Maytansinol, PDB code: 7e4z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Tubulin in Complex with Maytansinol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tubulin in Complex with Maytansinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.2 occ:1.00 O A:HOH641 2.0 28.4 1.0 O1G A:GTP501 2.0 20.5 1.0 O A:HOH630 2.0 27.5 1.0 O A:HOH640 2.1 25.1 1.0 O A:HOH633 2.1 33.1 1.0 O1B A:GTP501 2.2 21.4 1.0 PG A:GTP501 3.3 23.8 1.0 PB A:GTP501 3.3 18.7 1.0 HZ1 B:LYS254 3.3 40.7 1.0 HG2 A:GLU71 3.4 63.2 1.0 HB2 A:GLN11 3.6 33.2 1.0 O3B A:GTP501 3.6 30.2 1.0 HB2 A:ASP98 3.7 39.9 1.0 HG3 A:GLU71 3.7 63.2 1.0 OD2 A:ASP69 3.8 28.3 1.0 H A:GLN11 3.8 29.7 1.0 O2G A:GTP501 3.9 25.7 1.0 O3A A:GTP501 3.9 24.3 1.0 CG A:GLU71 4.0 52.7 1.0 OE1 A:GLU71 4.1 54.0 1.0 HB3 A:ASP98 4.1 39.9 1.0 NZ B:LYS254 4.1 34.0 1.0 HZ2 B:LYS254 4.2 40.7 1.0 CB A:ASP98 4.3 33.2 1.0 OD1 A:ASP69 4.3 43.2 1.0 HG1 A:THR145 4.4 33.5 1.0 HE21 A:GLN11 4.4 46.9 1.0 CB A:GLN11 4.4 27.7 1.0 O3G A:GTP501 4.5 25.3 1.0 OD2 A:ASP98 4.5 49.1 1.0 CG A:ASP69 4.5 34.2 1.0 CD A:GLU71 4.5 55.9 1.0 HB3 A:GLN11 4.5 33.2 1.0 N A:GLN11 4.5 24.7 1.0 HZ3 B:LYS254 4.6 40.7 1.0 O2B A:GTP501 4.6 26.7 1.0 CG A:ASP98 4.6 35.7 1.0 HA2 A:GLY10 4.7 28.8 1.0 OG1 A:THR145 4.8 27.9 1.0 HB A:THR145 4.8 36.0 1.0 O1A A:GTP501 4.9 25.2 1.0 NE2 A:GLN11 4.9 39.1 1.0 HE3 B:LYS254 4.9 42.6 1.0 PA A:GTP501 5.0 23.4 1.0 HG21 A:VAL74 5.0 61.2 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Tubulin in Complex with Maytansinol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Tubulin in Complex with Maytansinol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:21.8 occ:1.00 O B:HOH629 2.1 37.2 1.0 OE1 B:GLN11 2.2 49.6 1.0 O1A B:GDP501 2.2 29.1 1.0 O C:HOH699 2.3 36.7 1.0 O B:HOH658 2.4 38.5 1.0 O B:HOH635 2.7 39.2 1.0 O B:HOH637 2.7 31.2 1.0 CD B:GLN11 3.4 44.5 1.0 PA B:GDP501 3.4 18.8 1.0 HB3 B:GLN11 3.6 36.2 1.0 O3A B:GDP501 3.6 23.2 1.0 H8 B:GDP501 3.7 35.4 1.0 OD1 B:ASP179 3.9 49.1 1.0 HB2 B:GLN11 4.0 36.2 1.0 CB B:GLN11 4.1 30.2 1.0 OD1 B:ASN101 4.2 24.6 1.0 C5' B:GDP501 4.2 23.6 1.0 HE22 B:GLN11 4.3 51.3 1.0 CG B:GLN11 4.3 38.8 1.0 O5' B:GDP501 4.3 21.3 1.0 NE2 B:GLN11 4.3 42.8 1.0 HD22 B:ASN101 4.5 37.8 1.0 HG2 B:GLN11 4.5 46.6 1.0 O2A B:GDP501 4.6 22.6 1.0 O1B B:GDP501 4.6 21.6 1.0 C8 B:GDP501 4.7 29.5 1.0 PB B:GDP501 4.8 24.3 1.0 CG B:ASP179 4.8 48.2 1.0 OE1 C:GLU254 4.9 46.0 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Tubulin in Complex with Maytansinol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tubulin in Complex with Maytansinol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:66.4 occ:1.00 O B:HOH601 2.1 46.1 1.0 O B:HOH668 2.2 57.7 1.0 O B:HOH665 3.8 50.5 1.0 HB3 B:ASP116 3.9 58.8 1.0 OD1 B:ASP120 4.2 49.9 1.0 OD1 B:ASP116 4.4 83.9 1.0 OD2 B:ASP120 4.5 43.1 1.0 CB B:ASP116 4.8 49.0 1.0 CG B:ASP120 4.8 45.5 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Tubulin in Complex with Maytansinol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tubulin in Complex with Maytansinol within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:28.7 occ:1.00 O C:HOH606 2.0 25.8 1.0 O C:HOH628 2.1 30.1 1.0 O1B C:GTP501 2.1 27.0 1.0 O C:HOH610 2.1 26.2 1.0 O C:HOH619 2.1 23.6 1.0 O1G C:GTP501 2.1 22.2 1.0 PG C:GTP501 3.3 18.7 1.0 PB C:GTP501 3.3 16.2 1.0 HG2 C:GLU71 3.3 41.9 1.0 HZ1 D:LYS254 3.4 39.0 1.0 O3B C:GTP501 3.6 22.9 1.0 HB2 C:GLN11 3.6 28.9 1.0 HB2 C:ASP98 3.7 31.3 1.0 OD2 C:ASP69 3.7 21.8 1.0 HG3 C:GLU71 3.7 41.9 1.0 H C:GLN11 3.8 20.6 1.0 O2G C:GTP501 3.8 18.3 1.0 CG C:GLU71 3.9 34.9 1.0 OD1 C:ASP69 4.0 22.3 1.0 O3A C:GTP501 4.0 26.4 1.0 OE1 C:GLU71 4.0 41.8 1.0 HB3 C:ASP98 4.1 31.3 1.0 NZ D:LYS254 4.2 32.5 1.0 CG C:ASP69 4.2 23.1 1.0 CB C:ASP98 4.3 26.1 1.0 HG1 C:THR145 4.3 25.4 1.0 HZ2 D:LYS254 4.3 39.0 1.0 N C:GLN11 4.4 17.2 1.0 CB C:GLN11 4.4 24.1 1.0 CD C:GLU71 4.5 40.3 1.0 HB3 C:GLN11 4.5 28.9 1.0 O2B C:GTP501 4.5 20.5 1.0 O3G C:GTP501 4.5 17.7 1.0 HA2 C:GLY10 4.5 26.2 1.0 OD2 C:ASP98 4.5 32.2 1.0 HZ3 D:LYS254 4.6 39.0 1.0 HB C:THR145 4.7 26.3 1.0 OG1 C:THR145 4.7 21.1 1.0 CG C:ASP98 4.9 31.0 1.0 HG21 C:VAL74 4.9 35.4 1.0 OE1 C:GLN11 5.0 36.9 1.0 CA C:GLN11 5.0 21.7 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Tubulin in Complex with Maytansinol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Tubulin in Complex with Maytansinol within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:78.1 occ:1.00 O D:HOH729 2.1 79.4 1.0 O2B D:GTP602 2.1 59.6 1.0 O D:HOH710 2.2 58.7 1.0 O2G D:GTP602 2.2 70.4 1.0 O D:HOH706 2.3 86.9 1.0 O D:HOH704 2.4 72.6 1.0 O3G D:GTP602 2.8 71.4 1.0 PG D:GTP602 2.9 114.2 1.0 PB D:GTP602 3.1 61.0 1.0 HB3 D:GLN11 3.3 83.6 1.0 H D:GLN11 3.4 68.0 1.0 HB2 D:GLN11 3.4 83.6 1.0 O3B D:GTP602 3.5 58.2 1.0 O3A D:GTP602 3.6 55.6 1.0 CB D:GLN11 3.8 69.7 1.0 O2A D:GTP602 3.9 62.5 1.0 N D:GLN11 4.1 56.6 1.0 O1G D:GTP602 4.3 55.5 1.0 OE1 D:GLU71 4.4 96.5 1.0 PA D:GTP602 4.4 46.7 1.0 HG21 D:THR74 4.5 103.8 1.0 O1B D:GTP602 4.5 82.1 1.0 CA D:GLN11 4.6 61.0 1.0 HB3 D:GLU71 4.6 95.6 1.0 HG1 D:THR145 4.6 90.7 1.0 OD2 D:ASP69 4.6 53.9 1.0 HA2 D:GLY10 4.6 60.2 1.0 OD1 D:ASP69 4.6 52.0 1.0 HB2 D:GLU71 4.8 95.6 1.0 HB D:THR145 4.8 68.4 1.0 CD D:GLN11 4.9 72.1 1.0 CG D:GLN11 4.9 73.8 1.0 OG1 D:THR145 5.0 75.6 1.0

W.Li, M.Huang, Y.Li, A.Xia, L.Tan, Z.Zhang, Y.Wang, J.Yang. C3 Ester Side Chain Plays A Pivotal Role in the Antitumor Activity of Maytansinoids. Biochem.Biophys.Res.Commun. V. 566 197 2021.
ISSN: ESSN 1090-2104
PubMed: 34144258
DOI: 10.1016/J.BBRC.2021.05.071