Magnesium in PDB 7e4r: Crystal Structure of Tubulin in Complex with D-DM1-Sme

The structure of Crystal Structure of Tubulin in Complex with D-DM1-Sme, PDB code: 7e4r 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)	45.45 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.982, 157.229, 182.574, 90, 90, 90
R / Rfree (%)	22.4 / 26.5

The structure of Crystal Structure of Tubulin in Complex with D-DM1-Sme also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Tubulin in Complex with D-DM1-Sme (pdb code 7e4r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Tubulin in Complex with D-DM1-Sme, PDB code: 7e4r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Tubulin in Complex with D-DM1-Sme


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 D-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:21.1 occ:1.00 O A:HOH636 2.0 31.6 1.0 O A:HOH609 2.1 33.8 1.0 O A:HOH613 2.1 33.5 1.0 O2G A:GTP501 2.1 18.4 1.0 O A:HOH635 2.2 29.2 1.0 O1B A:GTP501 2.2 22.2 1.0 HZ1 B:LYS252 3.2 46.0 1.0 HB2 A:GLN11 3.3 46.2 1.0 PB A:GTP501 3.3 23.8 1.0 PG A:GTP501 3.4 23.8 1.0 O3A A:GTP501 3.7 31.6 1.0 O3B A:GTP501 3.8 45.9 1.0 H A:GLN11 3.8 40.5 1.0 NZ B:LYS252 4.0 38.4 1.0 HB3 A:GLN11 4.0 46.2 1.0 HZ2 B:LYS252 4.0 46.0 1.0 HB2 A:ASP98 4.0 38.0 1.0 CB A:GLN11 4.1 38.5 1.0 OE2 A:GLU71 4.1 49.7 1.0 O1G A:GTP501 4.2 26.2 1.0 HB3 A:ASP98 4.2 38.0 1.0 HB3 A:GLU71 4.2 56.5 1.0 OD1 A:ASP69 4.2 40.7 1.0 HZ3 B:LYS252 4.2 46.0 1.0 OE1 A:GLN11 4.4 38.6 1.0 OD2 A:ASP69 4.5 39.5 1.0 O3G A:GTP501 4.5 33.4 1.0 N A:GLN11 4.5 33.7 1.0 CB A:ASP98 4.5 31.7 1.0 O A:HOH608 4.6 35.5 1.0 HG21 A:VAL74 4.6 64.7 1.0 O2B A:GTP501 4.6 30.6 1.0 O1A A:GTP501 4.7 37.4 1.0 PA A:GTP501 4.7 24.1 1.0 OD2 A:ASP98 4.7 51.0 1.0 CG A:ASP69 4.8 39.9 1.0 HG1 A:THR145 4.8 34.8 1.0 CA A:GLN11 4.9 30.3 1.0 CD A:GLU71 4.9 56.1 1.0 CD A:GLN11 4.9 29.9 1.0 HG23 A:VAL74 5.0 64.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Tubulin in Complex with D-DM1-Sme


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 D-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:40.0 occ:1.00 O C:HOH612 2.0 47.1 1.0 O2A B:GDP501 2.1 36.1 1.0 OE1 B:GLN11 2.1 65.4 1.0 OD2 B:ASP177 3.3 70.0 1.0 CD B:GLN11 3.4 58.9 1.0 O B:HOH641 3.4 32.6 1.0 PA B:GDP501 3.6 24.2 1.0 H8 B:GDP501 3.6 54.7 1.0 HB3 B:GLN11 3.8 56.2 1.0 HE22 B:GLN11 4.1 61.0 1.0 C5' B:GDP501 4.2 26.5 1.0 HB2 B:GLN11 4.2 56.2 1.0 NE2 B:GLN11 4.2 50.8 1.0 OE1 C:GLU254 4.3 51.2 1.0 CB B:GLN11 4.3 46.9 1.0 O5' B:GDP501 4.3 17.9 1.0 O3A B:GDP501 4.3 22.2 1.0 OD1 B:ASN99 4.4 28.2 1.0 CG B:GLN11 4.4 47.1 1.0 CG B:ASP177 4.5 61.0 1.0 O1A B:GDP501 4.5 22.2 1.0 HD21 B:ASN99 4.6 31.6 1.0 O2B B:GDP501 4.6 38.8 1.0 C8 B:GDP501 4.6 45.5 1.0 HG2 B:GLN11 4.7 56.5 1.0 HB3 B:ASP177 4.8 62.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Tubulin in Complex with D-DM1-Sme


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 D-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:22.1 occ:1.00 O C:HOH620 2.0 23.3 1.0 O C:HOH619 2.0 24.7 1.0 O1G C:GTP501 2.1 19.9 1.0 O1B C:GTP501 2.1 24.8 1.0 O C:HOH654 2.1 31.8 1.0 O C:HOH638 2.1 29.3 1.0 HZ1 D:LYS252 3.2 35.8 1.0 HG2 C:GLU71 3.2 40.1 1.0 PB C:GTP501 3.3 19.8 1.0 PG C:GTP501 3.3 23.1 1.0 HB2 C:GLN11 3.4 27.9 1.0 O3B C:GTP501 3.7 24.8 1.0 OE2 C:GLU71 3.7 37.4 1.0 H C:GLN11 3.8 25.0 1.0 O3A C:GTP501 3.8 29.3 1.0 HB2 C:ASP98 3.8 33.6 1.0 HE21 C:GLN11 3.8 64.2 1.0 OD1 C:ASP69 3.9 18.5 1.0 CG C:GLU71 4.0 33.4 1.0 HG3 C:GLU71 4.0 40.1 1.0 O2G C:GTP501 4.0 23.1 1.0 NZ D:LYS252 4.0 29.8 1.0 HB3 C:ASP98 4.0 33.6 1.0 OD2 C:ASP69 4.1 25.1 1.0 HZ2 D:LYS252 4.1 35.8 1.0 CB C:GLN11 4.2 23.3 1.0 HB3 C:GLN11 4.3 27.9 1.0 HZ3 D:LYS252 4.3 35.8 1.0 CD C:GLU71 4.3 28.4 1.0 CB C:ASP98 4.3 28.0 1.0 NE2 C:GLN11 4.4 53.5 1.0 CG C:ASP69 4.4 22.3 1.0 O3G C:GTP501 4.5 24.3 1.0 N C:GLN11 4.5 20.9 1.0 O2B C:GTP501 4.5 22.7 1.0 HG1 C:THR145 4.5 27.4 1.0 OD2 C:ASP98 4.6 31.8 1.0 HE22 C:GLN11 4.7 64.2 1.0 HA2 C:GLY10 4.8 26.3 1.0 HG21 C:VAL74 4.8 39.3 1.0 O C:HOH662 4.9 44.9 1.0 PA C:GTP501 4.9 21.1 1.0 OG1 C:THR145 4.9 22.8 1.0 HB C:THR145 4.9 29.1 1.0 CG C:ASP98 4.9 35.8 1.0 O1A C:GTP501 4.9 27.2 1.0 CA C:GLN11 5.0 22.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Tubulin in Complex with D-DM1-Sme


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 D-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:73.5 occ:1.00 O2B D:GTP501 2.0 119.9 1.0 OE2 D:GLU69 2.3 123.5 1.0 O1G D:GTP501 2.7 106.0 1.0 HB2 D:GLN11 3.2 115.6 1.0 PB D:GTP501 3.2 108.0 1.0 PG D:GTP501 3.3 129.7 1.0 O2G D:GTP501 3.3 90.4 1.0 O3B D:GTP501 3.3 97.5 1.0 CD D:GLU69 3.4 105.1 1.0 H D:GLN11 3.7 85.8 1.0 HG2 D:GLU69 4.0 96.5 1.0 CB D:GLN11 4.0 96.3 1.0 HB3 D:GLN11 4.1 115.6 1.0 O3A D:GTP501 4.1 75.7 1.0 CG D:GLU69 4.3 80.4 1.0 OE1 D:GLU69 4.3 76.5 1.0 O1B D:GTP501 4.3 85.6 1.0 N D:GLN11 4.4 71.5 1.0 HG3 D:GLU69 4.5 96.5 1.0 OD1 D:ASP67 4.5 57.2 1.0 OE1 D:GLN11 4.6 77.2 1.0 OD2 D:ASP67 4.6 69.4 1.0 HG1 D:THR143 4.7 98.5 1.0 O3G D:GTP501 4.8 84.8 1.0 CA D:GLN11 4.8 84.4 1.0 O2A D:GTP501 4.9 74.2 1.0 CD D:GLN11 4.9 98.0 1.0 HA2 D:GLY10 4.9 82.9 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