Calcium in PDB 5ca1: Crystal Structure of T2R-Ttl-Nocodazole Complex

The structure of Crystal Structure of T2R-Ttl-Nocodazole Complex, PDB code: 5ca1 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)	41.52 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.440, 158.362, 180.692, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.5

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

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-Nocodazole Complex (pdb code 5ca1). 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-Nocodazole Complex, PDB code: 5ca1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-Nocodazole 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-Nocodazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:54.4 occ:1.00 O A:GLY44 2.3 48.1 1.0 OD2 A:ASP39 2.4 52.0 1.0 OE2 A:GLU55 2.5 52.2 1.0 OD1 A:ASP39 2.5 49.2 1.0 OG1 A:THR41 2.5 71.3 1.0 O A:THR41 2.5 63.0 1.0 OE1 A:GLU55 2.6 57.7 1.0 CG A:ASP39 2.8 55.9 1.0 CD A:GLU55 2.9 56.5 1.0 CB A:THR41 3.5 64.8 1.0 C A:GLY44 3.5 59.3 1.0 C A:THR41 3.5 66.8 1.0 CA A:THR41 3.9 61.5 1.0 N A:THR41 4.2 62.8 1.0 CA A:GLY45 4.3 63.0 1.0 N A:GLY45 4.3 55.3 1.0 CB A:ASP39 4.3 49.4 1.0 CZ A:PHE49 4.3 53.4 1.0 CG A:GLU55 4.4 57.2 1.0 N A:GLY44 4.4 55.3 1.0 CA A:GLY44 4.4 50.2 1.0 OD1 A:ASN50 4.5 65.7 1.0 OD2 A:ASP47 4.5 63.8 1.0 NE2 A:HIS61 4.6 58.2 1.0 N A:ILE42 4.7 66.3 1.0 CG2 A:THR41 4.8 57.1 1.0 CE1 A:PHE49 4.8 58.5 1.0 ND2 A:ASN50 4.9 53.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-Nocodazole 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-Nocodazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:45.7 occ:1.00 OG1 C:THR41 2.4 46.8 1.0 O C:GLY44 2.4 41.1 1.0 O C:THR41 2.4 54.0 1.0 OE2 C:GLU55 2.5 44.2 1.0 OD2 C:ASP39 2.5 42.4 1.0 OD1 C:ASP39 2.6 41.3 1.0 OE1 C:GLU55 2.6 43.7 1.0 CG C:ASP39 2.9 41.6 1.0 CD C:GLU55 2.9 40.9 1.0 C C:THR41 3.5 45.8 1.0 C C:GLY44 3.5 46.5 1.0 CB C:THR41 3.5 48.6 1.0 CA C:THR41 3.9 45.5 1.0 OD2 C:ASP47 4.1 58.9 1.0 CA C:GLY45 4.1 44.0 1.0 N C:THR41 4.2 46.7 1.0 N C:GLY45 4.2 47.3 1.0 O C:HOH611 4.4 41.9 1.0 CB C:ASP39 4.4 46.3 1.0 CG C:GLU55 4.4 35.4 1.0 OD1 C:ASN50 4.5 42.7 1.0 N C:GLY44 4.5 42.2 1.0 CA C:GLY44 4.6 46.6 1.0 CZ C:PHE49 4.6 32.8 1.0 NE2 C:HIS61 4.6 40.4 1.0 N C:ILE42 4.7 46.1 1.0 CG2 C:THR41 4.8 38.7 1.0 CE1 C:PHE49 4.8 39.4 1.0

Y.Wang, H.Zhang, B.Gigant, Y.Yu, Y.Wu, X.Chen, Q.Lai, Z.Yang, Q.Chen, J.Yang. Structures of A Diverse Set of Colchicine Binding Site Inhibitors in Complex with Tubulin Provide A Rationale For Drug Discovery. Febs J. V. 283 102 2016.
ISSN: ISSN 1742-464X
PubMed: 26462166
DOI: 10.1111/FEBS.13555