Magnesium in PDB 7en3: Crystal Structure of Tubulin in Complex with Tubulysin Analogue Tgl

The structure of Crystal Structure of Tubulin in Complex with Tubulysin Analogue Tgl, PDB code: 7en3 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)	40.06 / 2.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.607, 154.216, 186.865, 90, 90, 90
R / Rfree (%)	19.9 / 23.9

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

Calcium	(Ca)	2 atoms
Fluorine	(F)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Tubulin in Complex with Tubulysin Analogue Tgl (pdb code 7en3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Tubulin in Complex with Tubulysin Analogue Tgl, PDB code: 7en3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Tubulin in Complex with Tubulysin Analogue Tgl


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 Tubulysin Analogue Tgl within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.6 occ:1.00 O1G A:GTP501 2.0 22.2 1.0 O A:HOH617 2.0 24.5 1.0 O A:HOH625 2.1 21.1 1.0 O A:HOH606 2.1 24.3 1.0 O A:HOH636 2.1 16.7 1.0 O1B A:GTP501 2.2 23.5 1.0 PG A:GTP501 3.2 22.4 1.0 PB A:GTP501 3.3 23.8 1.0 O3G A:GTP501 3.5 22.8 1.0 O3B A:GTP501 3.6 23.9 1.0 O3A A:GTP501 3.9 25.4 1.0 NZ B:LYS252 4.0 34.8 1.0 OD1 A:ASP69 4.1 38.1 1.0 OD2 A:ASP69 4.1 42.4 1.0 CB A:GLN11 4.3 30.3 1.0 OD2 A:ASP98 4.4 34.0 1.0 OE1 A:GLU71 4.4 50.4 1.0 O2G A:GTP501 4.5 21.8 1.0 O1A A:GTP501 4.5 26.5 1.0 CB A:ASP98 4.5 35.7 1.0 N A:GLN11 4.6 29.6 1.0 CG A:ASP69 4.6 41.0 1.0 NE2 A:GLN11 4.6 31.3 1.0 O2B A:GTP501 4.7 24.0 1.0 CG A:ASP98 4.7 35.0 1.0 PA A:GTP501 4.8 27.1 1.0 CD A:GLU71 4.9 50.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Tubulin in Complex with Tubulysin Analogue Tgl


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 Tubulysin Analogue Tgl within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:45.0 occ:1.00 O B:HOH628 2.1 29.2 1.0 O B:HOH643 2.4 22.2 1.0 O B:HOH601 2.6 30.3 1.0 OE1 B:GLU69 2.9 44.6 1.0 O1B B:GDP501 3.0 22.6 1.0 O B:HOH632 3.4 37.6 1.0 O1A B:GDP501 3.7 23.4 1.0 O B:HOH609 3.7 20.6 1.0 O3A B:GDP501 3.8 22.9 1.0 NE2 B:GLN11 3.9 28.6 1.0 O B:HOH622 3.9 30.9 1.0 PB B:GDP501 3.9 23.5 1.0 O B:HOH610 3.9 37.1 1.0 CB B:GLN11 4.0 27.6 1.0 CD B:GLU69 4.0 46.7 1.0 O2B B:GDP501 4.3 23.4 1.0 PA B:GDP501 4.4 22.1 1.0 CD B:GLN11 4.4 28.4 1.0 OE2 B:GLU69 4.5 48.9 1.0 OD1 B:ASN99 4.8 23.3 1.0 CG B:GLN11 4.8 27.7 1.0 N B:GLN11 5.0 27.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Tubulin in Complex with Tubulysin Analogue Tgl


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 Tubulysin Analogue Tgl within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:27.3 occ:1.00 O3G C:GTP502 1.9 21.2 1.0 O1B C:GTP502 2.1 21.4 1.0 O C:HOH613 2.1 18.5 1.0 O C:HOH605 2.1 18.3 1.0 O C:HOH629 2.2 23.4 1.0 O C:HOH630 2.2 23.9 1.0 PG C:GTP502 3.0 21.4 1.0 PB C:GTP502 3.2 21.7 1.0 O1G C:GTP502 3.4 21.2 1.0 O3B C:GTP502 3.4 21.3 1.0 O3A C:GTP502 3.8 21.6 1.0 NZ D:LYS252 3.9 31.1 1.0 OD1 C:ASP69 4.1 30.2 1.0 OE1 C:GLU71 4.3 40.4 1.0 OD2 C:ASP69 4.3 29.9 1.0 O2G C:GTP502 4.4 21.2 1.0 CB C:ASP98 4.4 35.4 1.0 CB C:GLN11 4.4 27.3 1.0 O1A C:GTP502 4.5 22.2 1.0 O2B C:GTP502 4.5 21.8 1.0 OD2 C:ASP98 4.6 36.1 1.0 N C:GLN11 4.6 26.5 1.0 CG C:ASP69 4.7 30.4 1.0 CG C:ASP98 4.7 36.1 1.0 PA C:GTP502 4.7 21.7 1.0 CB C:GLU71 5.0 37.4 1.0 OG1 C:THR145 5.0 26.1 1.0

W.Li, L.Tan, Z.Zhang, Q.Xia, D.Lei, Y.Li, T.Zhang, S.Zeng, X.Sima, Y.Wang. The X-Ray Structure of Tubulysin Analogue Tgl in Complex with Tubulin and Three Possible Routes For the Development of Next-Generation Tubulysin Analogues. Biochem.Biophys.Res.Commun. V. 565 29 2021.
ISSN: ESSN 1090-2104
PubMed: 34090207
DOI: 10.1016/J.BBRC.2021.05.086