Calcium in PDB 5h7o: Crystal Structure of Dj-101 in Complex with Tubulin Protein

The structure of Crystal Structure of Dj-101 in Complex with Tubulin Protein, PDB code: 5h7o was solved by K.Arnst, Y.Wang, D.-J.Hwang, Y.Xue, T.Costello, D.Hamilton, Q.Chen, J.Yang, F.Park, J.T.Dalton, D.D.Miller, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.199, 157.029, 182.576, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.6

The structure of Crystal Structure of Dj-101 in Complex with Tubulin Protein also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Dj-101 in Complex with Tubulin Protein (pdb code 5h7o). 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 Dj-101 in Complex with Tubulin Protein, PDB code: 5h7o:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Dj-101 in Complex with Tubulin Protein


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 Dj-101 in Complex with Tubulin Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:73.5 occ:1.00 O A:GLY44 2.5 69.8 1.0 OE2 A:GLU55 2.6 63.5 1.0 OG1 A:THR41 2.7 79.0 1.0 OD2 A:ASP39 2.8 60.2 1.0 OD1 A:ASP39 2.9 59.4 1.0 O A:THR41 3.0 78.1 1.0 CG A:ASP39 3.2 62.2 1.0 OE1 A:GLU55 3.4 66.3 1.0 CD A:GLU55 3.4 65.5 1.0 C A:GLY44 3.5 73.6 1.0 CB A:THR41 3.8 75.5 1.0 OD1 A:ASN50 3.8 64.0 1.0 CA A:GLY45 3.9 74.8 1.0 C A:THR41 4.0 76.7 1.0 N A:GLY45 4.1 74.2 1.0 OD2 A:ASP47 4.2 58.0 1.0 CZ A:PHE49 4.3 78.8 1.0 CA A:THR41 4.3 75.8 1.0 ND2 A:ASN50 4.4 64.2 1.0 CG A:ASN50 4.5 64.0 1.0 N A:THR41 4.6 73.6 1.0 CA A:GLY44 4.7 73.2 1.0 CB A:ASP39 4.7 64.6 1.0 C A:GLY45 4.8 74.0 1.0 N A:GLY44 4.8 73.0 1.0 CG A:GLU55 4.8 65.6 1.0 CE1 A:PHE49 4.9 76.9 1.0 NE2 A:HIS61 4.9 76.1 1.0 CG A:ASP47 5.0 61.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Dj-101 in Complex with Tubulin Protein


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 Dj-101 in Complex with Tubulin Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:66.8 occ:1.00 OE2 C:GLU55 2.3 47.5 1.0 OG1 C:THR41 2.3 70.1 1.0 O C:GLY44 2.6 57.0 1.0 OD1 C:ASP39 2.7 58.0 1.0 O C:THR41 2.7 62.9 1.0 OD2 C:ASP39 2.8 54.1 1.0 CG C:ASP39 3.1 56.9 1.0 CD C:GLU55 3.3 47.0 1.0 OD2 C:ASP47 3.4 57.1 1.0 C C:GLY44 3.4 58.7 1.0 CB C:THR41 3.5 66.9 1.0 OE1 C:GLU55 3.6 49.5 1.0 C C:THR41 3.7 63.6 1.0 CA C:GLY45 3.9 58.8 1.0 OD1 C:ASN50 3.9 41.3 1.0 N C:GLY45 4.0 58.7 1.0 CA C:THR41 4.0 65.3 1.0 N C:THR41 4.4 64.0 1.0 CA C:GLY44 4.5 59.8 1.0 CZ C:PHE49 4.5 41.3 1.0 ND2 C:ASN50 4.6 40.1 1.0 CB C:ASP39 4.6 58.7 1.0 CG C:GLU55 4.6 45.3 1.0 CG C:ASP47 4.7 54.4 1.0 CG C:ASN50 4.7 39.3 1.0 CG2 C:THR41 4.7 66.2 1.0 CE1 C:PHE49 4.7 41.2 1.0 N C:GLY44 4.8 60.5 1.0 C C:GLY45 4.8 58.5 1.0 N C:ILE42 4.9 64.0 1.0

K.E.Arnst, Y.Wang, D.J.Hwang, Y.Xue, T.Costello, D.Hamilton, Q.Chen, J.Yang, F.Park, J.T.Dalton, D.D.Miller, W.Li. A Potent, Metabolically Stable Tubulin Inhibitor Targets the Colchicine Binding Site and Overcomes Taxane Resistance. Cancer Res. V. 78 265 2018.
ISSN: ESSN 1538-7445
PubMed: 29180476
DOI: 10.1158/0008-5472.CAN-17-0577