Calcium in PDB 5ca0: Crystal Structure of T2R-Ttl-Lexibulin Complex

The structure of Crystal Structure of T2R-Ttl-Lexibulin Complex, PDB code: 5ca0 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)	38.70 / 2.50
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 (%)	19.8 / 23.7

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

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-Lexibulin Complex (pdb code 5ca0). 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-Lexibulin Complex, PDB code: 5ca0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-Lexibulin 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-Lexibulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:81.8 occ:1.00 OE2 A:GLU55 2.4 68.0 1.0 OG1 A:THR41 2.4 0.8 1.0 OD1 A:ASP39 2.5 70.2 1.0 O A:GLY44 2.5 70.2 1.0 OD2 A:ASP39 2.5 77.5 1.0 O A:HOH604 2.5 77.0 1.0 O A:THR41 2.6 0.7 1.0 OE1 A:GLU55 2.7 83.2 1.0 CG A:ASP39 2.8 74.2 1.0 CD A:GLU55 2.9 79.1 1.0 HZ A:PHE49 3.2 0.8 1.0 HB A:THR41 3.3 0.8 1.0 CB A:THR41 3.4 93.2 1.0 HA3 A:GLY45 3.4 0.8 1.0 C A:GLY44 3.5 85.1 1.0 C A:THR41 3.6 0.4 1.0 HD21 A:ASN50 3.8 92.7 1.0 H A:THR41 3.9 0.8 1.0 CA A:THR41 4.0 86.7 1.0 CZ A:PHE49 4.0 93.2 1.0 H A:GLY44 4.1 99.6 1.0 CA A:GLY45 4.3 99.0 1.0 N A:GLY45 4.3 81.9 1.0 CB A:ASP39 4.3 68.5 1.0 N A:THR41 4.4 88.1 1.0 CG A:GLU55 4.4 80.4 1.0 OD2 A:ASP47 4.5 74.3 1.0 OD1 A:ASN50 4.5 90.3 1.0 CA A:GLY44 4.5 89.0 1.0 HE2 A:PHE49 4.5 94.2 1.0 ND2 A:ASN50 4.6 77.3 1.0 O A:HOH623 4.6 65.2 1.0 NE2 A:HIS61 4.6 90.9 1.0 HB2 A:ASP39 4.6 82.2 1.0 HA2 A:GLY44 4.6 0.9 1.0 N A:GLY44 4.6 83.0 1.0 CG2 A:THR41 4.7 68.9 1.0 CE2 A:PHE49 4.7 78.5 1.0 HG2 A:GLU55 4.7 96.5 1.0 HG3 A:GLU55 4.8 96.5 1.0 HB3 A:ASP39 4.8 82.2 1.0 HG21 A:THR41 4.8 82.7 1.0 HE1 A:PHE49 4.8 0.2 1.0 N A:ILE42 4.8 0.2 1.0 CE1 A:PHE49 4.9 99.3 1.0 HA2 A:GLY45 4.9 0.8 1.0 HA A:THR41 4.9 0.1 1.0 HA A:ILE42 4.9 0.4 1.0 CG A:ASN50 5.0 62.8 1.0 HA A:ASP39 5.0 98.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-Lexibulin 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-Lexibulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:71.2 occ:1.00 OE2 C:GLU55 2.4 73.2 1.0 O C:THR41 2.4 86.8 1.0 OD2 C:ASP39 2.4 69.3 1.0 OG1 C:THR41 2.5 87.0 1.0 OE1 C:GLU55 2.5 65.9 1.0 O C:HOH601 2.5 62.4 1.0 O C:GLY44 2.5 83.4 1.0 OD1 C:ASP39 2.6 76.4 1.0 CD C:GLU55 2.8 69.3 1.0 CG C:ASP39 2.9 65.2 1.0 HA3 C:GLY45 3.2 86.6 1.0 C C:GLY44 3.4 76.5 1.0 C C:THR41 3.5 68.4 1.0 CB C:THR41 3.5 78.9 1.0 HB C:THR41 3.5 94.7 1.0 HZ C:PHE49 3.8 55.6 1.0 H C:GLY44 3.8 81.6 1.0 HD21 C:ASN50 3.9 61.3 1.0 CA C:THR41 4.0 80.1 1.0 N C:GLY45 4.0 75.6 1.0 H C:THR41 4.0 96.7 1.0 CA C:GLY45 4.0 72.2 1.0 OD2 C:ASP47 4.3 77.7 1.0 CA C:GLY44 4.3 83.8 1.0 CG C:GLU55 4.3 68.1 1.0 N C:THR41 4.3 80.6 1.0 CB C:ASP39 4.4 71.3 1.0 N C:GLY44 4.4 68.0 1.0 HA2 C:GLY44 4.4 0.6 1.0 OD1 C:ASN50 4.4 75.7 1.0 HE1 C:PHE49 4.4 85.7 1.0 HA2 C:GLY45 4.5 86.6 1.0 CZ C:PHE49 4.5 46.4 1.0 HA C:ILE42 4.6 73.5 1.0 HG3 C:GLU55 4.7 81.8 1.0 N C:ILE42 4.7 75.4 1.0 HG2 C:GLU55 4.7 81.8 1.0 ND2 C:ASN50 4.7 51.1 1.0 NE2 C:HIS61 4.7 60.4 1.0 HB2 C:ASP39 4.7 85.6 1.0 H C:GLY45 4.7 90.7 1.0 HB3 C:ASP39 4.8 85.6 1.0 CG2 C:THR41 4.8 84.0 1.0 HA C:THR41 4.9 96.2 1.0 CE1 C:PHE49 4.9 71.4 1.0 HG21 C:THR41 4.9 0.8 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