Calcium 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:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-Erianin Complex (pdb code 8wd0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of T2R-Ttl-Erianin Complex, PDB code: 8wd0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-Erianin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of T2R-Ttl-Erianin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:76.9 occ:0.00 OD2 A:ASP39 2.3 71.7 1.0 O A:GLY44 2.3 73.5 1.0 OG1 A:THR41 2.4 84.6 1.0 O A:THR41 2.5 79.5 1.0 OE1 A:GLU55 2.6 82.3 1.0 OE2 A:GLU55 2.6 80.4 1.0 OD1 A:ASP39 2.6 79.5 1.0 CG A:ASP39 2.8 75.6 1.0 CD A:GLU55 2.9 78.6 1.0 C A:GLY44 3.4 73.0 1.0 C A:THR41 3.5 81.1 1.0 CB A:THR41 3.5 81.2 1.0 OD2 A:ASP47 3.9 68.2 1.0 CA A:THR41 4.0 83.9 1.0 CA A:GLY45 4.1 73.7 1.0 N A:GLY45 4.1 69.2 1.0 N A:THR41 4.3 80.9 1.0 CB A:ASP39 4.3 72.6 1.0 N A:GLY44 4.4 77.0 1.0 CZ A:PHE49 4.4 71.3 1.0 OD1 A:ASN50 4.4 71.3 1.0 CA A:GLY44 4.4 78.6 1.0 CG A:GLU55 4.4 74.1 1.0 N A:ILE42 4.7 78.6 1.0 ND2 A:ASN50 4.8 74.3 1.0 CG2 A:THR41 4.8 74.8 1.0 NE2 A:HIS61 4.8 73.4 1.0 CE1 A:PHE49 4.8 73.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-Erianin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of T2R-Ttl-Erianin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:65.6 occ:0.00 OD2 C:ASP39 2.3 63.8 1.0 O C:GLY44 2.3 65.2 1.0 OG1 C:THR41 2.4 70.2 1.0 OE1 C:GLU55 2.4 68.5 1.0 OE2 C:GLU55 2.4 70.1 1.0 O C:THR41 2.4 73.7 1.0 OD1 C:ASP39 2.5 63.4 1.0 CG C:ASP39 2.7 62.0 1.0 CD C:GLU55 2.8 67.9 1.0 C C:GLY44 3.4 65.0 1.0 C C:THR41 3.5 68.1 1.0 CB C:THR41 3.5 67.6 1.0 CA C:THR41 3.9 63.5 1.0 CA C:GLY45 4.0 70.1 1.0 N C:GLY45 4.1 61.2 1.0 OD2 C:ASP47 4.1 74.9 1.0 N C:THR41 4.2 57.4 1.0 CB C:ASP39 4.3 61.6 1.0 CG C:GLU55 4.3 56.4 1.0 O C:HOH605 4.4 58.7 1.0 N C:GLY44 4.4 62.0 1.0 OD1 C:ASN50 4.5 62.5 1.0 CA C:GLY44 4.5 65.3 1.0 CZ C:PHE49 4.6 57.9 1.0 N C:ILE42 4.7 70.6 1.0 NE2 C:HIS61 4.8 59.0 1.0 CG2 C:THR41 4.8 63.6 1.0 ND2 C:ASN50 4.8 49.9 1.0 CE1 C:PHE49 4.8 57.6 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