Zinc in PDB 2o8m: Crystal Structure of the S139A Mutant of Hepatitis C Virus NS3/4A Protease

The structure of Crystal Structure of the S139A Mutant of Hepatitis C Virus NS3/4A Protease, PDB code: 2o8m was solved by T.O.Fischmann, A.J.Prongay, V.M.Madison, N.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	224.640, 224.640, 75.360, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 22.8

The structure of Crystal Structure of the S139A Mutant of Hepatitis C Virus NS3/4A Protease also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the S139A Mutant of Hepatitis C Virus NS3/4A Protease (pdb code 2o8m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the S139A Mutant of Hepatitis C Virus NS3/4A Protease, PDB code: 2o8m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the S139A Mutant of Hepatitis C Virus NS3/4A Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the S139A Mutant of Hepatitis C Virus NS3/4A Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:38.1 occ:1.00 SG A:CYS97 2.1 34.1 1.0 O A:HOH1116 2.3 15.2 1.0 SG A:CYS145 2.4 33.5 1.0 SG A:CYS99 2.5 45.1 1.0 CB A:CYS145 3.1 29.6 1.0 CB A:CYS97 3.3 31.1 1.0 CB A:CYS99 3.4 41.4 1.0 N A:CYS99 3.6 41.9 1.0 CA A:CYS97 3.8 31.6 1.0 N A:THR98 3.9 37.8 1.0 CA A:CYS99 4.0 41.3 1.0 C A:CYS97 4.2 37.9 1.0 CB A:HIS149 4.4 33.5 1.0 CA A:CYS145 4.6 29.3 1.0 C A:CYS99 4.6 44.3 1.0 N A:GLY100 4.6 40.4 1.0 CB A:ALA147 4.6 31.2 1.0 C A:THR98 4.7 45.1 1.0 CD2 A:HIS149 4.8 39.7 1.0 CA A:THR98 4.9 38.8 1.0 CG A:HIS149 4.9 37.6 1.0 N A:SER101 5.0 38.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the S139A Mutant of Hepatitis C Virus NS3/4A Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the S139A Mutant of Hepatitis C Virus NS3/4A Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:37.9 occ:1.00 SG B:CYS145 2.2 31.7 1.0 O B:HOH292 2.3 14.6 1.0 SG B:CYS97 2.4 34.8 1.0 SG B:CYS99 2.5 41.3 1.0 CB B:CYS145 3.1 27.9 1.0 CB B:CYS97 3.3 31.4 1.0 CB B:CYS99 3.4 37.8 1.0 N B:CYS99 3.6 38.7 1.0 CA B:CYS97 3.8 31.9 1.0 N B:THR98 3.9 36.3 1.0 CA B:CYS99 4.0 38.1 1.0 C B:CYS97 4.2 37.8 1.0 CB B:HIS149 4.3 27.2 1.0 CB B:ALA147 4.4 30.3 1.0 CA B:CYS145 4.5 27.9 1.0 N B:GLY100 4.7 38.5 1.0 C B:CYS99 4.7 42.0 1.0 ND1 B:HIS149 4.7 31.9 1.0 C B:THR98 4.7 42.2 1.0 CG B:HIS149 4.8 30.2 1.0 N B:ALA147 4.8 30.0 1.0 CD B:PRO146 5.0 31.2 1.0 CA B:THR98 5.0 36.7 1.0

A.J.Prongay, Z.Guo, N.Yao, J.Pichardo, T.Fischmann, C.Strickland, J.Myers, P.C.Weber, B.M.Beyer, R.Ingram, Z.Hong, W.W.Prosise, L.Ramanathan, S.S.Taremi, T.Yarosh-Tomaine, R.Zhang, M.Senior, R.S.Yang, B.Malcolm, A.Arasappan, F.Bennett, S.L.Bogen, K.Chen, E.Jao, Y.T.Liu, R.G.Lovey, A.K.Saksena, S.Venkatraman, V.Girijavallabhan, F.G.Njoroge, V.Madison. Discovery of the Hcv NS3/4A Protease Inhibitor (1R,5S)-N-[3-Amino-1-(Cyclobutylmethyl)-2,3-Dioxopropyl]-3- [2(S)-[[[(1,1-Dimethylethyl)Amino]Carbonyl]Amino]-3, 3-Dimethyl-1-Oxobutyl]- 6,6-Dimethyl-3-Azabicyclo[3.1.0]Hexan-2(S)-Carboxamide (Sch 503034) II. Key Steps in Structure-Based Optimization J.Med.Chem. V. 50 2310 2007.
ISSN: ISSN 0022-2623
PubMed: 17444623
DOI: 10.1021/JM060173K