Magnesium in PDB 7e4q: Crystal Structure of Tubulin in Complex with L-DM1-Sme

The structure of Crystal Structure of Tubulin in Complex with L-DM1-Sme, PDB code: 7e4q 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)	46.88 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.893, 157.209, 181.658, 90, 90, 90
R / Rfree (%)	20.5 / 25.2

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

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

The binding sites of Magnesium atom in the Crystal Structure of Tubulin in Complex with L-DM1-Sme (pdb code 7e4q). 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 L-DM1-Sme, PDB code: 7e4q:
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 L-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 L-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:43.3 occ:1.00 O A:HOH609 2.1 52.1 1.0 O A:HOH641 2.1 47.4 1.0 O3G A:GTP501 2.1 29.9 1.0 O1B A:GTP501 2.2 36.3 1.0 O A:HOH634 2.2 39.9 1.0 O A:HOH629 2.2 48.3 1.0 HZ1 B:LYS254 3.1 70.8 1.0 HB2 A:GLN11 3.3 48.1 1.0 PB A:GTP501 3.3 40.3 1.0 PG A:GTP501 3.3 43.4 1.0 O3A A:GTP501 3.7 55.7 1.0 O3B A:GTP501 3.8 53.9 1.0 H A:GLN11 3.8 52.3 1.0 O1G A:GTP501 3.9 44.9 1.0 NZ B:LYS254 3.9 59.0 1.0 HB2 A:ASP98 4.0 58.1 1.0 OE1 A:GLU71 4.0 63.4 1.0 HZ2 B:LYS254 4.0 70.8 1.0 OD1 A:ASP69 4.1 42.6 1.0 CB A:GLN11 4.1 40.1 1.0 HB3 A:GLN11 4.2 48.1 1.0 HB3 A:GLU71 4.2 74.3 1.0 HZ3 B:LYS254 4.2 70.8 1.0 HB3 A:ASP98 4.2 58.1 1.0 OD2 A:ASP69 4.3 49.5 1.0 N A:GLN11 4.5 43.6 1.0 CB A:ASP98 4.5 48.5 1.0 OE1 A:GLN11 4.5 61.1 1.0 O2G A:GTP501 4.6 42.3 1.0 O2B A:GTP501 4.6 50.6 1.0 OD2 A:ASP98 4.6 55.7 1.0 CG A:ASP69 4.7 49.1 1.0 O1A A:GTP501 4.7 38.7 1.0 HG1 A:THR145 4.7 54.0 1.0 PA A:GTP501 4.8 39.6 1.0 CG A:ASP98 4.8 50.2 1.0 CA A:GLN11 4.9 48.1 1.0 HA2 A:GLY10 4.9 51.9 1.0 HG21 A:VAL74 5.0 67.2 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Tubulin in Complex with L-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 L-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:45.5 occ:1.00 O1A B:GDP501 2.1 50.0 1.0 O B:HOH646 2.2 44.9 1.0 O C:HOH605 2.3 51.9 1.0 O B:HOH627 2.3 52.4 1.0 OE1 B:GLN11 2.6 47.1 1.0 O B:HOH653 2.6 51.3 1.0 O B:HOH655 2.8 41.3 1.0 CD B:GLN11 3.3 61.1 1.0 PA B:GDP501 3.5 35.9 1.0 HB3 B:GLN11 3.5 53.1 1.0 H8 B:GDP501 3.7 56.0 1.0 HE22 B:GLN11 3.7 86.0 1.0 NE2 B:GLN11 3.8 71.7 1.0 OD2 B:ASP179 3.9 54.4 1.0 HB2 B:GLN11 3.9 53.1 1.0 CB B:GLN11 4.1 44.2 1.0 O3A B:GDP501 4.1 44.2 1.0 CG B:GLN11 4.3 58.4 1.0 C5' B:GDP501 4.4 39.5 1.0 OE1 C:GLU254 4.4 72.1 1.0 O5' B:GDP501 4.4 32.5 1.0 O2A B:GDP501 4.5 35.5 1.0 HE21 B:GLN11 4.5 86.0 1.0 OD1 B:ASN101 4.6 47.9 1.0 C8 B:GDP501 4.6 46.7 1.0 O3B B:GDP501 4.7 44.0 1.0 HG2 B:GLN11 4.7 70.0 1.0 HD21 B:ASN101 4.8 45.4 1.0 CG B:ASP179 4.9 59.2 1.0 HG3 B:GLN11 4.9 70.0 1.0 PB B:GDP501 5.0 41.5 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Tubulin in Complex with L-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 L-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:36.0 occ:1.00 O C:HOH622 2.0 38.1 1.0 O C:HOH636 2.0 34.6 1.0 O C:HOH619 2.1 34.9 1.0 O1G C:GTP501 2.1 29.6 1.0 O C:HOH650 2.1 40.5 1.0 O1B C:GTP501 2.2 34.6 1.0 PG C:GTP501 3.3 38.6 1.0 PB C:GTP501 3.3 53.9 1.0 HZ1 D:LYS254 3.4 53.2 1.0 HG2 C:GLU71 3.4 65.4 1.0 HB2 C:GLN11 3.5 41.3 1.0 O3B C:GTP501 3.7 45.1 1.0 H C:GLN11 3.7 40.9 1.0 OD1 C:ASP69 3.8 37.9 1.0 O2G C:GTP501 3.8 39.5 1.0 OE1 C:GLU71 3.8 63.5 1.0 HG3 C:GLU71 3.8 65.4 1.0 HB2 C:ASP98 3.8 49.4 1.0 O3A C:GTP501 3.8 45.9 1.0 OD2 C:ASP69 3.9 36.8 1.0 CG C:GLU71 4.0 54.5 1.0 NZ D:LYS254 4.2 44.3 1.0 HB3 C:ASP98 4.2 49.4 1.0 HZ2 D:LYS254 4.2 53.2 1.0 CG C:ASP69 4.3 37.7 1.0 CB C:GLN11 4.3 34.4 1.0 CD C:GLU71 4.4 58.1 1.0 CB C:ASP98 4.4 41.1 1.0 N C:GLN11 4.4 34.1 1.0 OD2 C:ASP98 4.4 43.2 1.0 HB3 C:GLN11 4.5 41.3 1.0 HZ3 D:LYS254 4.5 53.2 1.0 O3G C:GTP501 4.5 33.0 1.0 HG1 C:THR145 4.5 43.9 1.0 O2B C:GTP501 4.6 42.2 1.0 HA2 C:GLY10 4.7 45.8 1.0 HG21 C:VAL74 4.7 57.4 1.0 OE1 C:GLN11 4.8 50.7 1.0 CG C:ASP98 4.8 43.0 1.0 O1A C:GTP501 4.9 36.2 1.0 HB C:THR145 4.9 45.1 1.0 PA C:GTP501 4.9 34.2 1.0 OG1 C:THR145 4.9 36.6 1.0 CA C:GLN11 5.0 35.6 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Tubulin in Complex with L-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 L-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:67.2 occ:1.00 O D:HOH602 2.0 87.7 1.0 O D:HOH611 2.1 78.5 1.0 O D:HOH617 2.1 86.5 1.0 O3G D:GTP502 2.5 65.9 1.0 O2B D:GTP502 2.7 60.4 1.0 O1G D:GTP502 3.0 64.3 1.0 PG D:GTP502 3.3 88.2 1.0 HB2 D:GLN11 3.3 107.1 1.0 OE2 D:GLU71 3.6 108.6 1.0 H D:GLN11 3.6 87.7 1.0 HB3 D:GLN11 3.7 107.1 1.0 PB D:GTP502 3.8 56.0 1.0 HB3 D:GLU71 3.9 103.3 1.0 HB2 D:GLU71 4.0 103.3 1.0 O3B D:GTP502 4.0 72.4 1.0 CB D:GLN11 4.0 89.2 1.0 OD1 D:ASP69 4.1 64.8 1.0 OD2 D:ASP69 4.3 67.8 1.0 N D:GLN11 4.3 73.1 1.0 HE21 D:GLN11 4.3 104.9 1.0 CB D:GLU71 4.4 86.1 1.0 O3A D:GTP502 4.4 60.8 1.0 HG1 D:THR145 4.5 98.3 1.0 O1A D:GTP502 4.5 78.2 1.0 O2G D:GTP502 4.6 55.3 1.0 NE2 D:GLN11 4.6 87.5 1.0 CD D:GLU71 4.6 111.4 1.0 HG2 D:GLU71 4.6 123.7 1.0 CG D:ASP69 4.6 69.4 1.0 HA2 D:GLY10 4.7 79.8 1.0 CA D:GLN11 4.7 77.8 1.0 HG1 D:THR74 4.7 115.0 1.0 CG D:GLU71 4.8 103.0 1.0 HE22 D:GLN11 4.9 104.9 1.0 HA D:GLN11 4.9 93.4 1.0 HB D:THR145 4.9 79.1 1.0 OG1 D:THR145 5.0 81.9 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Tubulin in Complex with L-DM1-Sme


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 L-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:114.2 occ:1.00 HD21 F:ASN333 2.5 134.4 1.0 HD22 F:ASN333 2.7 134.4 1.0 O1B F:ACP402 2.8 160.1 1.0 ND2 F:ASN333 3.0 112.0 1.0 OE2 F:GLU331 3.3 123.6 1.0 HZ2 F:LYS74 3.4 138.7 1.0 OE1 F:GLU331 3.4 111.0 1.0 O2G F:ACP402 3.5 142.8 1.0 CD F:GLU331 3.7 110.7 1.0 HZ1 F:LYS74 3.8 138.7 1.0 NZ F:LYS74 3.9 115.6 1.0 HZ3 F:LYS74 4.0 138.7 1.0 PB F:ACP402 4.2 198.4 1.0 CG F:ASN333 4.3 102.9 1.0 HA F:ASN333 4.7 74.9 1.0 PG F:ACP402 4.8 182.5 1.0 O2B F:ACP402 4.9 153.8 1.0 OD1 F:ASN333 5.0 109.1 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