Magnesium in PDB 5ezy: Crystal Structure of T2R-Ttl-Taccalonolide Aj Complex

The structure of Crystal Structure of T2R-Ttl-Taccalonolide Aj Complex, PDB code: 5ezy was solved by Y.Wang, Y.Yu, Q.Chen, J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.20 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.304, 158.505, 180.809, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 20.8

The structure of Crystal Structure of T2R-Ttl-Taccalonolide Aj Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Taccalonolide Aj Complex (pdb code 5ezy). 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 T2R-Ttl-Taccalonolide Aj Complex, PDB code: 5ezy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-Taccalonolide Aj Complex


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 T2R-Ttl-Taccalonolide Aj Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:18.9 occ:1.00 O A:HOH839 2.1 13.6 1.0 O A:HOH636 2.1 18.5 1.0 O1G A:GTP501 2.1 14.5 1.0 O A:HOH761 2.1 18.4 1.0 O A:HOH658 2.1 15.4 1.0 O1B A:GTP501 2.1 16.7 1.0 HZ1 B:LYS254 3.1 31.0 1.0 PG A:GTP501 3.3 17.3 1.0 PB A:GTP501 3.3 18.1 1.0 HB2 A:GLN11 3.5 21.2 1.0 O3B A:GTP501 3.7 20.9 1.0 H A:GLN11 3.7 20.4 1.0 O3G A:GTP501 3.7 17.2 1.0 O3A A:GTP501 3.7 20.4 1.0 HB2 A:ASP98 3.9 27.2 1.0 NZ B:LYS254 3.9 25.8 1.0 HZ2 B:LYS254 3.9 31.0 1.0 OE1 A:GLU71 4.0 40.4 1.0 OD1 A:ASP69 4.0 18.4 1.0 HB3 A:GLN11 4.1 21.2 1.0 HB3 A:ASP98 4.2 27.2 1.0 HZ3 B:LYS254 4.2 31.0 1.0 OD2 A:ASP69 4.2 18.9 1.0 CB A:GLN11 4.2 17.7 1.0 HB3 A:GLU71 4.3 43.0 1.0 OD2 A:ASP98 4.3 20.7 1.0 CB A:ASP98 4.4 22.6 1.0 N A:GLN11 4.4 17.0 1.0 HE21 A:GLN11 4.5 26.2 1.0 O2G A:GTP501 4.5 16.8 1.0 O A:HOH800 4.5 53.4 1.0 O A:HOH614 4.5 35.9 1.0 O2B A:GTP501 4.6 19.7 1.0 CG A:ASP69 4.6 18.5 1.0 O1A A:GTP501 4.6 15.2 1.0 CG A:ASP98 4.8 21.3 1.0 HB A:THR145 4.8 21.1 1.0 PA A:GTP501 4.8 17.4 1.0 HG1 A:THR145 4.8 21.7 1.0 HA2 A:GLY10 4.8 22.5 1.0 NE2 A:GLN11 4.9 21.8 1.0 CA A:GLN11 4.9 17.1 1.0 HE3 B:LYS254 4.9 32.6 1.0 CE B:LYS254 5.0 27.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-Taccalonolide Aj Complex


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 T2R-Ttl-Taccalonolide Aj Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:11.0 occ:1.00 OE1 B:GLN11 2.2 27.0 1.0 O1A B:GDP501 2.2 19.0 1.0 O B:HOH708 2.3 19.4 1.0 O C:HOH843 2.3 29.2 1.0 O B:HOH615 2.4 25.6 1.0 O B:HOH750 2.5 22.7 1.0 CD B:GLN11 3.4 26.9 1.0 PA B:GDP501 3.6 17.4 1.0 HB3 B:GLN11 3.6 24.8 1.0 H8 B:GDP501 3.7 25.5 1.0 OD2 B:ASP179 3.9 23.4 1.0 O3A B:GDP501 3.9 14.4 1.0 HB2 B:GLN11 4.0 24.8 1.0 CB B:GLN11 4.1 20.7 1.0 CG B:GLN11 4.3 23.5 1.0 C5' B:GDP501 4.4 18.6 1.0 O B:HOH840 4.4 48.5 1.0 O C:HOH726 4.4 37.1 1.0 HE22 B:GLN11 4.4 33.7 1.0 NE2 B:GLN11 4.4 28.1 1.0 HG2 B:GLN11 4.4 28.2 1.0 O5' B:GDP501 4.4 16.7 1.0 OD1 B:ASN101 4.5 22.9 1.0 OE1 C:GLU254 4.6 26.8 1.0 HD21 B:ASN101 4.6 25.1 1.0 O1B B:GDP501 4.6 15.4 1.0 O2A B:GDP501 4.6 17.0 1.0 C8 B:GDP501 4.6 21.2 1.0 O B:HOH721 4.7 41.9 1.0 CG B:ASP179 4.9 25.0 1.0 PB B:GDP501 4.9 16.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-Taccalonolide Aj Complex


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 T2R-Ttl-Taccalonolide Aj Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:15.5 occ:1.00 O1B C:GTP501 2.0 13.6 1.0 O1G C:GTP501 2.1 13.3 1.0 O C:HOH657 2.1 11.6 1.0 O C:HOH902 2.1 12.8 1.0 O C:HOH677 2.2 13.9 1.0 O C:HOH861 2.2 16.6 1.0 HZ1 D:LYS254 3.2 21.2 1.0 PB C:GTP501 3.2 14.2 1.0 PG C:GTP501 3.2 15.4 1.0 HB2 C:GLN11 3.4 14.1 1.0 O3B C:GTP501 3.6 16.2 1.0 H C:GLN11 3.6 14.8 1.0 O3G C:GTP501 3.6 14.5 1.0 O3A C:GTP501 3.7 17.7 1.0 HG2 C:GLU71 3.7 31.4 1.0 HB2 C:ASP98 3.9 21.2 1.0 NZ D:LYS254 4.0 17.6 1.0 OD1 C:ASP69 4.0 14.7 1.0 HZ2 D:LYS254 4.1 21.2 1.0 HG3 C:GLU71 4.1 31.4 1.0 OE1 C:GLU71 4.1 32.0 1.0 HB3 C:GLN11 4.1 14.1 1.0 CB C:GLN11 4.2 11.7 1.0 OD2 C:ASP69 4.2 13.1 1.0 HZ3 D:LYS254 4.3 21.2 1.0 CG C:GLU71 4.3 26.1 1.0 HB3 C:ASP98 4.3 21.2 1.0 N C:GLN11 4.3 12.3 1.0 O2B C:GTP501 4.5 16.4 1.0 O2G C:GTP501 4.5 12.7 1.0 CB C:ASP98 4.5 17.7 1.0 O1A C:GTP501 4.5 14.9 1.0 OD2 C:ASP98 4.6 19.1 1.0 CG C:ASP69 4.6 15.1 1.0 PA C:GTP501 4.7 14.6 1.0 O C:HOH605 4.7 26.0 1.0 HA2 C:GLY10 4.7 16.2 1.0 CD C:GLU71 4.7 29.2 1.0 HB C:THR145 4.8 18.8 1.0 HG1 C:THR145 4.8 22.1 1.0 CA C:GLN11 4.9 12.4 1.0 CG C:ASP98 4.9 18.6 1.0 OE1 C:GLN11 4.9 23.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-Taccalonolide Aj Complex


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 T2R-Ttl-Taccalonolide Aj Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:33.2 occ:1.00 O D:HOH715 2.0 29.4 1.0 O1G D:GTP501 2.1 37.4 1.0 O D:HOH679 2.1 31.0 1.0 O D:HOH620 2.1 32.3 1.0 O1B D:GTP501 2.3 25.4 1.0 PG D:GTP501 3.2 40.9 1.0 PB D:GTP501 3.4 28.3 1.0 HG3 D:GLU71 3.4 75.8 1.0 HB2 D:GLN11 3.4 30.4 1.0 O3G D:GTP501 3.5 38.1 1.0 H D:GLN11 3.6 31.9 1.0 O3B D:GTP501 3.7 38.4 1.0 O3A D:GTP501 3.7 20.1 1.0 HB2 D:GLU71 3.8 65.8 1.0 O D:HOH738 3.9 39.9 1.0 HG2 D:GLU71 4.0 75.8 1.0 CG D:GLU71 4.0 63.2 1.0 HE21 D:GLN11 4.1 52.6 1.0 HB3 D:GLN11 4.1 30.4 1.0 CB D:GLN11 4.2 25.4 1.0 O D:HOH603 4.3 44.0 1.0 N D:GLN11 4.3 26.6 1.0 OD2 D:ASP69 4.4 32.9 1.0 OD1 D:ASP69 4.4 34.6 1.0 CB D:GLU71 4.4 54.8 1.0 O2G D:GTP501 4.5 37.8 1.0 HA3 D:GLY98 4.5 57.3 1.0 O1A D:GTP501 4.6 29.9 1.0 NE2 D:GLN11 4.7 43.8 1.0 HA2 D:GLY10 4.7 35.6 1.0 O2B D:GTP501 4.7 29.9 1.0 PA D:GTP501 4.7 28.3 1.0 HG1 D:THR145 4.8 40.8 1.0 CA D:GLN11 4.9 25.5 1.0 HB3 D:GLU71 4.9 65.8 1.0 CG D:ASP69 4.9 33.4 1.0 HG21 D:THR74 4.9 73.5 1.0 HA2 D:GLY98 4.9 57.3 1.0 HB D:THR145 5.0 39.8 1.0 HE22 D:GLN11 5.0 52.6 1.0

Y.Wang, Y.Yu, G.B.Li, S.A.Li, C.Wu, B.Gigant, W.Qin, H.Chen, Y.Wu, Q.Chen, J.Yang. Mechanism of Microtubule Stabilization By Taccalonolide Aj Nat Commun V. 8 15787 2017.
ISSN: ESSN 2041-1723
PubMed: 28585532
DOI: 10.1038/NCOMMS15787