Magnesium 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:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Dj-101 in Complex with Tubulin Protein, PDB code: 5h7o:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Dj-101 in Complex with Tubulin Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg502 b:32.9 occ:1.00 O2G A:GTP501 1.8 31.1 1.0 O A:HOH605 2.0 0.4 1.0 O A:HOH604 2.2 60.0 1.0 O2B A:GTP501 2.4 30.6 1.0 O A:HOH601 2.6 60.9 1.0 PG A:GTP501 3.0 31.9 1.0 PB A:GTP501 3.3 30.8 1.0 O3B A:GTP501 3.5 32.2 1.0 O3G A:GTP501 3.6 32.1 1.0 O3A A:GTP501 3.9 31.7 1.0 NZ B:LYS252 4.0 49.0 1.0 CB A:ASP98 4.1 41.4 1.0 OD1 A:ASP69 4.2 47.2 1.0 OD2 A:ASP98 4.3 40.6 1.0 O1G A:GTP501 4.3 32.0 1.0 CG A:ASP98 4.5 40.6 1.0 OE1 A:GLU71 4.5 54.0 1.0 OD2 A:ASP69 4.6 49.6 1.0 CB A:GLN11 4.6 37.7 1.0 O1B A:GTP501 4.7 31.3 1.0 N A:GLN11 4.8 36.9 1.0 O2A A:GTP501 4.8 32.2 1.0 OG1 A:THR145 4.9 31.9 1.0 CG A:ASP69 4.9 49.0 1.0 CD A:GLU71 4.9 52.6 1.0 OE1 A:GLN11 5.0 36.3 1.0 PA A:GTP501 5.0 31.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Dj-101 in Complex with Tubulin Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 B:Mg502 b:33.1 occ:1.00 OE1 B:GLN11 2.3 41.3 1.0 O2A B:GDP501 2.4 27.6 1.0 O C:HOH606 2.6 30.0 1.0 O B:HOH606 2.8 28.4 1.0 O B:HOH605 2.9 39.1 1.0 OD2 B:ASP177 3.2 49.9 1.0 CD B:GLN11 3.6 41.0 1.0 PA B:GDP501 3.7 26.7 1.0 O3A B:GDP501 4.0 28.6 1.0 OD1 B:ASN99 4.1 30.3 1.0 CG B:ASP177 4.2 48.7 1.0 C5' B:GDP501 4.3 28.7 1.0 NE2 B:GLN11 4.4 41.9 1.0 OE1 C:GLU254 4.4 38.8 1.0 O5' B:GDP501 4.4 27.2 1.0 CB B:GLN11 4.5 37.7 1.0 CG B:GLN11 4.6 39.4 1.0 CB B:ASP177 4.8 46.3 1.0 CG B:ASN99 5.0 29.6 1.0 O1A B:GDP501 5.0 28.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Dj-101 in Complex with Tubulin Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Dj-101 in Complex with Tubulin Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:29.5 occ:1.00 O3G C:GTP501 2.0 25.5 1.0 O C:HOH602 2.0 32.8 1.0 O2B C:GTP501 2.0 26.9 1.0 O C:HOH603 2.1 20.5 1.0 O C:HOH604 2.2 31.1 1.0 O C:HOH601 2.2 26.2 1.0 PG C:GTP501 3.1 26.1 1.0 PB C:GTP501 3.2 27.0 1.0 O3B C:GTP501 3.5 26.6 1.0 O2G C:GTP501 3.6 26.3 1.0 O3A C:GTP501 3.7 27.6 1.0 NZ D:LYS252 3.9 44.6 1.0 OE1 C:GLU71 3.9 41.6 1.0 OD1 C:ASP69 4.0 30.7 1.0 CB C:GLN11 4.3 30.8 1.0 OD2 C:ASP69 4.4 32.8 1.0 CB C:ASP98 4.4 37.2 1.0 O1G C:GTP501 4.4 26.1 1.0 O1B C:GTP501 4.5 27.7 1.0 N C:GLN11 4.5 28.8 1.0 O2A C:GTP501 4.6 28.5 1.0 OD2 C:ASP98 4.6 36.9 1.0 PA C:GTP501 4.7 27.6 1.0 CG C:ASP69 4.7 32.4 1.0 NE2 C:GLN11 4.7 33.3 1.0 CG C:ASP98 4.8 36.8 1.0 CE D:LYS252 4.9 43.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Dj-101 in Complex with Tubulin Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Dj-101 in Complex with Tubulin Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:49.8 occ:1.00 O2G D:GTP501 2.5 60.7 1.0 O3G D:GTP501 2.8 61.7 1.0 O2B D:GTP501 2.9 62.3 1.0 PG D:GTP501 3.1 64.1 1.0 OD2 D:ASP67 3.8 66.0 1.0 OD1 D:ASP67 3.8 66.3 1.0 CB D:GLU69 3.9 80.3 1.0 O3B D:GTP501 3.9 64.2 1.0 PB D:GTP501 3.9 65.8 1.0 CB D:GLN11 4.1 69.4 1.0 CG D:ASP67 4.2 66.2 1.0 O3A D:GTP501 4.3 62.0 1.0 N D:GLN11 4.3 64.4 1.0 CG D:GLU69 4.5 81.6 1.0 O1G D:GTP501 4.5 61.5 1.0 NE2 D:GLN11 4.7 71.5 1.0 CA D:GLN11 4.7 66.2 1.0 CG2 D:THR72 4.8 0.4 1.0 O2A D:GTP501 4.9 62.3 1.0 CG D:GLN11 4.9 70.5 1.0 OG1 D:THR143 4.9 66.3 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