Calcium in PDB 5c8y: Crystal Structure of T2R-Ttl-Plinabulin Complex

The structure of Crystal Structure of T2R-Ttl-Plinabulin Complex, PDB code: 5c8y 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)	39.70 / 2.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.060, 158.444, 181.825, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 27.1

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

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-Plinabulin Complex (pdb code 5c8y). 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-Plinabulin Complex, PDB code: 5c8y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-Plinabulin 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-Plinabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:76.7 occ:1.00 OG1 A:THR41 2.4 0.8 1.0 OE2 A:GLU55 2.4 91.2 1.0 O A:THR41 2.5 83.5 1.0 OD1 A:ASP39 2.5 67.5 1.0 OE1 A:GLU55 2.5 48.5 1.0 O A:GLY44 2.5 50.4 1.0 OD2 A:ASP39 2.6 82.4 1.0 CD A:GLU55 2.8 75.0 1.0 CG A:ASP39 2.9 77.4 1.0 HB A:THR41 3.4 0.2 1.0 CB A:THR41 3.4 0.2 1.0 C A:GLY44 3.4 68.7 1.0 HA3 A:GLY45 3.5 74.6 1.0 C A:THR41 3.5 85.2 1.0 HZ A:PHE49 3.7 78.5 1.0 H A:GLY44 3.8 84.2 1.0 CA A:THR41 3.9 82.9 1.0 HD21 A:ASN50 3.9 69.0 1.0 H A:THR41 3.9 0.1 1.0 N A:GLY45 4.2 69.5 1.0 CA A:GLY45 4.3 62.1 1.0 CA A:GLY44 4.3 84.5 1.0 CG A:GLU55 4.3 94.7 1.0 N A:THR41 4.3 91.8 1.0 N A:GLY44 4.4 70.2 1.0 HA2 A:GLY44 4.4 0.3 1.0 CB A:ASP39 4.4 77.5 1.0 CZ A:PHE49 4.5 65.4 1.0 OD1 A:ASN50 4.6 60.5 1.0 NE2 A:HIS61 4.6 77.4 1.0 OD2 A:ASP47 4.6 59.5 1.0 N A:ILE42 4.7 56.4 1.0 HA A:ILE42 4.7 98.2 1.0 CG2 A:THR41 4.7 62.9 1.0 HG2 A:GLU55 4.7 0.6 1.0 HG3 A:GLU55 4.7 0.6 1.0 ND2 A:ASN50 4.7 57.5 1.0 HG21 A:THR41 4.8 75.5 1.0 HB3 A:ASP39 4.8 93.0 1.0 HA A:THR41 4.8 99.4 1.0 HA2 A:GLY45 4.8 74.6 1.0 HE2 A:PHE49 4.8 84.5 1.0 HB2 A:ASP39 4.8 93.0 1.0 H A:GLY45 5.0 83.4 1.0 HA A:ASP39 5.0 90.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-Plinabulin 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-Plinabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:55.6 occ:1.00 OG1 C:THR41 2.4 72.7 1.0 OE2 C:GLU55 2.5 68.6 1.0 OD1 C:ASP39 2.5 40.7 1.0 OD2 C:ASP39 2.5 49.2 1.0 O C:THR41 2.5 69.9 1.0 OE1 C:GLU55 2.6 38.8 1.0 O C:GLY44 2.7 67.0 1.0 CG C:ASP39 2.8 53.4 1.0 CD C:GLU55 2.9 62.3 1.0 HA3 C:GLY45 3.1 62.7 1.0 C C:GLY44 3.5 60.3 1.0 CB C:THR41 3.5 58.5 1.0 C C:THR41 3.6 50.7 1.0 HB C:THR41 3.6 70.2 1.0 HZ C:PHE49 3.7 54.7 1.0 OD2 C:ASP47 3.9 76.4 1.0 HD21 C:ASN50 3.9 41.1 1.0 CA C:GLY45 4.0 52.2 1.0 H C:THR41 4.0 57.8 1.0 CA C:THR41 4.0 54.8 1.0 N C:GLY45 4.0 62.7 1.0 H C:GLY44 4.1 63.4 1.0 N C:THR41 4.3 48.1 1.0 CB C:ASP39 4.3 60.1 1.0 HE1 C:PHE49 4.4 58.3 1.0 CG C:GLU55 4.4 55.6 1.0 HA2 C:GLY45 4.4 62.7 1.0 OD1 C:ASN50 4.4 36.7 1.0 CZ C:PHE49 4.5 45.6 1.0 CA C:GLY44 4.5 51.0 1.0 HA2 C:GLY44 4.6 61.3 1.0 HB2 C:ASP39 4.6 72.1 1.0 N C:GLY44 4.6 52.9 1.0 O C:HOH656 4.7 40.2 1.0 ND2 C:ASN50 4.7 34.3 1.0 HA C:ILE42 4.7 75.8 1.0 HG3 C:GLU55 4.7 66.7 1.0 N C:ILE42 4.7 45.7 1.0 NE2 C:HIS61 4.8 37.8 1.0 H C:GLY45 4.8 75.3 1.0 CG2 C:THR41 4.8 32.6 1.0 HB3 C:ASP39 4.8 72.1 1.0 CE1 C:PHE49 4.8 48.6 1.0 HG2 C:GLU55 4.8 66.7 1.0 HG21 C:THR41 4.9 39.2 1.0 HA C:THR41 4.9 65.7 1.0 HG23 C:THR41 5.0 39.2 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