Calcium 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:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of T2R-Ttl-Taccalonolide Aj Complex, PDB code: 5ezy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-Taccalonolide Aj 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-Taccalonolide Aj Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:37.4 occ:1.00 O A:THR41 2.4 47.6 1.0 O A:GLY44 2.4 36.2 1.0 OD1 A:ASP39 2.4 42.3 1.0 OG1 A:THR41 2.4 41.1 1.0 O A:HOH621 2.5 31.2 1.0 OD2 A:ASP39 2.5 44.6 1.0 OE1 A:GLU55 2.5 44.8 1.0 OE2 A:GLU55 2.5 42.0 1.0 CG A:ASP39 2.8 42.9 1.0 CD A:GLU55 2.8 43.0 1.0 HA3 A:GLY45 3.3 58.4 1.0 CB A:THR41 3.4 44.3 1.0 C A:THR41 3.4 48.9 1.0 HB A:THR41 3.4 53.2 1.0 C A:GLY44 3.5 40.8 1.0 H A:GLY44 3.7 53.1 1.0 HZ A:PHE49 3.8 48.7 1.0 H A:THR41 3.8 65.4 1.0 CA A:THR41 3.9 49.5 1.0 HD21 A:ASN50 4.0 35.7 1.0 CA A:GLY45 4.2 48.6 1.0 N A:THR41 4.2 54.5 1.0 N A:GLY45 4.2 44.4 1.0 O A:HOH619 4.3 38.0 1.0 CB A:ASP39 4.3 42.2 1.0 CG A:GLU55 4.3 40.3 1.0 N A:GLY44 4.4 44.2 1.0 HE1 A:PHE49 4.4 46.7 1.0 CA A:GLY44 4.5 43.1 1.0 OD2 A:ASP47 4.6 45.5 1.0 CZ A:PHE49 4.6 40.6 1.0 HA2 A:GLY45 4.6 58.4 1.0 N A:ILE42 4.6 47.7 1.0 HB3 A:ASP39 4.6 50.6 1.0 HG2 A:GLU55 4.7 48.4 1.0 OD1 A:ASN50 4.7 32.6 1.0 NE2 A:HIS61 4.7 45.4 1.0 HA A:ILE42 4.7 54.8 1.0 HB2 A:ASP39 4.7 50.6 1.0 HG3 A:GLU55 4.7 48.4 1.0 CG2 A:THR41 4.8 42.5 1.0 HA A:THR41 4.8 59.3 1.0 ND2 A:ASN50 4.8 29.8 1.0 HA2 A:GLY44 4.9 51.7 1.0 H A:GLY43 4.9 48.7 1.0 HG21 A:THR41 4.9 51.0 1.0 CE1 A:PHE49 4.9 38.9 1.0 HA A:ASP39 5.0 54.5 1.0 O A:HOH865 5.0 38.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-Taccalonolide Aj 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-Taccalonolide Aj Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:26.5 occ:1.00 O C:THR41 2.4 30.7 1.0 OG1 C:THR41 2.4 37.6 1.0 OD2 C:ASP39 2.4 31.2 1.0 O C:GLY44 2.4 33.0 1.0 OE1 C:GLU55 2.5 25.2 1.0 OE2 C:GLU55 2.5 25.6 1.0 O C:HOH618 2.5 22.2 1.0 OD1 C:ASP39 2.5 30.3 1.0 CD C:GLU55 2.8 24.4 1.0 CG C:ASP39 2.8 30.8 1.0 C C:THR41 3.4 32.7 1.0 HA3 C:GLY45 3.4 45.3 1.0 CB C:THR41 3.4 38.9 1.0 C C:GLY44 3.5 35.4 1.0 HB C:THR41 3.6 46.7 1.0 H C:THR41 3.7 46.0 1.0 H C:GLY44 3.8 39.4 1.0 CA C:THR41 3.9 36.3 1.0 HZ C:PHE49 3.9 34.6 1.0 HD21 C:ASN50 4.1 22.0 1.0 N C:THR41 4.2 38.3 1.0 CA C:GLY45 4.2 37.8 1.0 N C:GLY45 4.3 38.0 1.0 O C:HOH642 4.3 43.0 1.0 HE1 C:PHE49 4.3 31.1 1.0 CG C:GLU55 4.3 21.7 1.0 CB C:ASP39 4.3 31.1 1.0 O C:HOH629 4.4 31.2 1.0 N C:GLY44 4.4 32.8 1.0 CA C:GLY44 4.5 34.2 1.0 OD2 C:ASP47 4.5 36.6 1.0 NE2 C:HIS61 4.6 23.7 1.0 N C:ILE42 4.6 32.2 1.0 HA C:ILE42 4.6 39.7 1.0 OD1 C:ASN50 4.6 20.7 1.0 CZ C:PHE49 4.7 28.8 1.0 HB3 C:ASP39 4.7 37.4 1.0 HG2 C:GLU55 4.7 26.0 1.0 HA2 C:GLY45 4.7 45.3 1.0 HG3 C:GLU55 4.7 26.0 1.0 CG2 C:THR41 4.7 41.2 1.0 HA2 C:GLY44 4.8 41.0 1.0 HB2 C:ASP39 4.8 37.4 1.0 HA C:THR41 4.8 43.6 1.0 CE1 C:PHE49 4.8 25.9 1.0 ND2 C:ASN50 4.8 18.4 1.0 HG21 C:THR41 4.9 49.5 1.0 HG23 C:THR41 5.0 49.5 1.0 O C:HOH846 5.0 31.6 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