Magnesium in PDB 8wd0: Crystal Structure of T2R-Ttl-Erianin Complex

The structure of Crystal Structure of T2R-Ttl-Erianin Complex, PDB code: 8wd0 was solved by J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.26 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	156.56, 181.54, 104.74, 90, 90, 90
R / Rfree (%)	22.7 / 25.8

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

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Erianin Complex (pdb code 8wd0). 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-Erianin Complex, PDB code: 8wd0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-Erianin 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-Erianin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:56.5 occ:0.00 O1G A:GTP501 2.0 55.8 0.0 O1B A:GTP501 2.2 52.7 0.0 PG A:GTP501 3.4 53.8 0.0 PB A:GTP501 3.4 52.0 0.0 O3B A:GTP501 3.7 52.1 0.0 O3A A:GTP501 3.8 52.5 0.0 OE1 A:GLU71 3.8 73.1 1.0 CG A:GLU71 4.0 60.1 1.0 OD2 A:ASP98 4.0 58.8 1.0 O2G A:GTP501 4.1 53.9 0.0 CB A:GLN11 4.1 46.9 1.0 OD1 A:ASP69 4.1 54.9 1.0 OD2 A:ASP69 4.2 56.5 1.0 CB A:ASP98 4.3 62.1 1.0 CD A:GLU71 4.4 62.8 1.0 N A:GLN11 4.4 46.0 1.0 O3G A:GTP501 4.4 53.4 0.0 OE1 A:GLN11 4.5 56.9 1.0 CG A:ASP98 4.5 54.5 1.0 NZ B:LYS252 4.6 76.3 1.0 CG A:ASP69 4.6 58.6 1.0 O2B A:GTP501 4.6 51.8 0.0 CA A:GLN11 4.8 50.1 1.0 OG1 A:THR145 4.9 51.2 1.0 O1A A:GTP501 4.9 53.0 0.0 PA A:GTP501 5.0 52.4 0.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-Erianin 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-Erianin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:59.4 occ:0.00 O1A B:GDP504 2.0 54.7 0.0 NE2 B:GLN11 3.4 72.6 1.0 PA B:GDP504 3.5 51.6 0.0 OD2 B:ASP177 3.5 67.0 1.0 CD B:GLN11 3.7 76.0 1.0 OE1 B:GLN11 3.9 75.4 1.0 O3A B:GDP504 4.1 49.5 0.0 C5' B:GDP504 4.2 53.4 0.0 CB B:GLN11 4.3 50.5 1.0 O5' B:GDP504 4.3 51.0 0.0 OD1 B:ASN99 4.4 49.4 1.0 O1B B:GDP504 4.4 51.1 0.0 CG B:ASP177 4.4 69.2 1.0 O2A B:GDP504 4.4 51.6 0.0 CG B:GLN11 4.5 64.3 1.0 C8 B:GDP504 4.9 55.2 0.0 PB B:GDP504 4.9 48.6 0.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-Erianin 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-Erianin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:46.6 occ:0.00 O1G C:GTP501 2.2 48.1 0.0 O1B C:GTP501 2.2 44.7 0.0 PB C:GTP501 3.4 44.4 0.0 PG C:GTP501 3.5 46.7 0.0 OE1 C:GLU71 3.5 53.7 1.0 O3A C:GTP501 3.7 45.0 0.0 O3B C:GTP501 3.8 45.1 0.0 CB C:GLN11 3.9 35.7 1.0 O2G C:GTP501 4.1 47.1 0.0 OE1 C:GLN11 4.1 51.5 1.0 OD2 C:ASP69 4.1 47.9 1.0 OD1 C:ASP69 4.2 51.8 1.0 OD2 C:ASP98 4.3 56.8 1.0 N C:GLN11 4.3 33.6 1.0 CB C:ASP98 4.6 44.8 1.0 O1A C:GTP501 4.6 46.1 0.0 CG C:ASP69 4.6 48.6 1.0 O3G C:GTP501 4.6 47.6 0.0 O2B C:GTP501 4.7 43.9 0.0 CA C:GLN11 4.7 37.5 1.0 PA C:GTP501 4.7 44.7 0.0 CD C:GLU71 4.7 59.0 1.0 OD1 D:ASN247 4.8 92.9 1.0 CD C:GLN11 4.8 45.8 1.0 CG C:ASP98 4.8 46.5 1.0 CG D:ASN247 4.9 94.2 1.0 CG C:GLN11 5.0 40.7 1.0 CB D:ASN247 5.0 87.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-Erianin 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-Erianin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:83.3 occ:0.00 O2G D:GTP501 2.1 82.9 0.0 O1B D:GTP501 2.3 80.7 0.0 PG D:GTP501 2.9 82.7 0.0 O1G D:GTP501 2.9 83.9 0.0 PB D:GTP501 3.2 80.3 0.0 O3A D:GTP501 3.4 80.5 0.0 O3B D:GTP501 3.6 80.4 0.0 CB D:GLN11 4.0 85.1 1.0 O3G D:GTP501 4.3 82.9 0.0 O1A D:GTP501 4.3 81.2 0.0 PA D:GTP501 4.4 80.2 0.0 OE1 D:GLN11 4.4 91.7 1.0 N D:GLN11 4.5 78.7 1.0 O2B D:GTP501 4.6 79.2 0.0 CB D:GLU69 4.8 85.1 1.0 OD1 D:ASP67 4.8 74.8 1.0 CA D:GLN11 4.9 81.5 1.0 O2A D:GTP501 4.9 79.6 0.0 OG1 D:THR143 5.0 89.8 1.0

W.Yan, Y.Zhou, X.Yuan, P.Bai, M.Tang, L.Chen, H.Wei, J.Yang. The Cytotoxic Natural Compound Erianin Binds to Colchicine Site of Beta-Tubulin and Overcomes Taxane Resistance Bioorg.Chem. V. 150 07569 2024.
ISSN: ISSN 0045-2068
PubMed: 38905886
DOI: 10.1016/J.BIOORG.2024.107569