Magnesium in PDB 3gol: Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D

All present enzymatic activity of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D:
2.7.7.48;

The structure of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D, PDB code: 3gol was solved by O.Nyanguile, H.De Bondt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.81 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.048, 106.620, 134.679, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 25

The structure of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D (pdb code 3gol). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D, PDB code: 3gol:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg580 b:55.7 occ:1.00 O A:HOH645 2.0 27.5 1.0 OD1 A:ASP220 2.1 58.0 1.0 O A:HOH647 2.3 45.5 1.0 O A:THR221 2.3 48.7 1.0 O A:HOH646 3.1 25.3 1.0 O A:HOH648 3.1 29.9 1.0 CG A:ASP220 3.2 50.5 1.0 C A:THR221 3.4 49.9 1.0 N A:THR221 3.6 48.9 1.0 O A:ARG222 3.7 57.5 1.0 OD2 A:ASP220 3.8 62.5 1.0 CA A:THR221 4.1 48.8 1.0 C A:ASP220 4.3 47.0 1.0 C A:ARG222 4.4 53.5 1.0 CB A:ASP220 4.5 46.6 1.0 N A:ARG222 4.5 50.9 1.0 CA A:ASP220 4.5 45.4 1.0 OD1 A:ASP318 4.7 42.4 1.0 N A:PHE224 4.8 45.5 1.0 OG1 A:THR221 4.8 48.5 1.0 CA A:ARG222 4.8 52.1 1.0 CG A:ASP318 4.9 48.3 1.0 CB A:THR221 4.9 47.9 1.0

Magnesium binding site 2 out of 2 in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg580 b:40.2 occ:1.00 O B:HOH585 1.9 32.4 1.0 O B:THR221 2.4 43.1 1.0 O B:HOH618 2.5 20.6 1.0 O B:HOH619 2.5 41.4 1.0 O B:HOH620 2.7 17.2 1.0 OD2 B:ASP220 3.0 49.6 1.0 N B:THR221 3.5 40.5 1.0 C B:THR221 3.5 44.0 1.0 CB B:ASP220 3.6 40.9 1.0 OD2 B:ASP318 3.6 49.8 1.0 CG B:ASP220 3.7 46.4 1.0 C B:ASP220 3.9 38.7 1.0 CA B:ASP220 4.0 38.8 1.0 CA B:THR221 4.1 42.0 1.0 N B:ARG222 4.6 46.5 1.0 CG B:ASP318 4.8 45.4 1.0 O B:ASP220 4.8 34.3 1.0 N B:CYS223 4.8 45.7 1.0 CA B:ARG222 4.8 47.0 1.0 OD1 B:ASP220 4.9 58.7 1.0 OD2 B:ASP319 5.0 60.2 1.0 OG1 B:THR221 5.0 48.6 1.0

D.Mcgowan, O.Nyanguile, M.D.Cummings, S.Vendeville, K.Vandyck, W.Van Den Broeck, C.W.Boutton, H.De Bondt, L.Quirynen, K.Amssoms, J.F.Bonfanti, S.Last, K.Rombauts, A.Tahri, L.Hu, F.Delouvroy, K.Vermeiren, G.Vandercruyssen, L.Van Der Helm, E.Cleiren, W.Mostmans, P.Lory, G.Pille, K.Van Emelen, G.Fanning, F.Pauwels, T.I.Lin, K.Simmen, P.Raboisson. 1,5-Benzodiazepine Inhibitors of Hcv NS5B Polymerase. Bioorg.Med.Chem.Lett. V. 19 2492 2009.
ISSN: ISSN 0960-894X
PubMed: 19342234
DOI: 10.1016/J.BMCL.2009.03.035