Sodium 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:

Zinc

(Zn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the S139A Mutant of Hepatitis C Virus NS3/4A Protease, PDB code: 2o8m:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na1002 b:23.1 occ:1.00 O A:ALA111 2.3 27.9 1.0 O A:ALA5 2.3 28.0 1.0 O A:HOH1024 2.3 35.0 1.0 O B:HOH246 2.4 39.4 1.0 O A:HOH1008 2.4 25.1 1.0 C A:ALA5 3.4 28.7 1.0 C A:ALA111 3.4 28.5 1.0 N A:ALA5 4.0 26.4 1.0 CB A:ALA111 4.0 27.3 1.0 O A:HOH1066 4.1 51.6 1.0 CA A:ALA5 4.1 25.6 1.0 O B:HOH285 4.1 52.8 1.0 N A:ASP112 4.3 25.0 1.0 CA A:ALA111 4.3 26.7 1.0 CA A:ASP112 4.3 24.6 1.0 CB A:ALA5 4.4 26.2 1.0 N A:TYR6 4.5 24.7 1.0 NH1 B:ARG92 4.5 72.9 1.0 OD1 A:ASP112 4.7 32.6 1.0 O A:HOH1005 4.7 19.1 1.0 CA A:TYR6 4.7 24.4 1.0 O B:HOH207 4.7 31.5 1.0 NH2 B:ARG92 4.8 72.3 1.0 O A:HIS110 4.9 29.6 1.0 O D:HOH242 4.9 26.1 1.0

Sodium 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 Sodium with other atoms in the Na 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 C:Na1001 b:21.4 occ:1.00 O C:GLY233 2.4 28.5 1.0 O A:HOH1022 2.4 32.6 1.0 O C:LEU231 2.4 28.9 1.0 O A:THR4 2.4 30.8 1.0 OG1 A:THR4 2.5 25.4 1.0 O C:HOH1002 2.5 23.2 1.0 C A:THR4 3.2 31.1 1.0 C C:LEU231 3.2 29.8 1.0 C C:GLY233 3.5 30.3 1.0 N C:GLY233 3.6 28.8 1.0 CB A:THR4 3.6 27.3 1.0 N A:THR4 3.6 26.7 1.0 CA A:THR4 3.7 26.4 1.0 CA C:LEU231 3.9 24.6 1.0 NZ C:LYS234 3.9 66.6 1.0 CA C:GLY233 4.0 27.9 1.0 C C:SER232 4.1 32.2 1.0 N C:SER232 4.1 27.9 1.0 O D:SER232 4.2 28.9 1.0 N A:ALA5 4.2 26.4 1.0 CA C:SER232 4.4 27.9 1.0 O C:VAL230 4.6 25.2 1.0 N C:LYS234 4.6 27.6 1.0 CA A:ALA5 4.7 25.6 1.0 O A:HOH1111 4.7 50.0 1.0 O A:MET-2 4.7 56.4 1.0 CG2 A:THR4 4.8 26.1 1.0 O C:SER232 4.8 31.6 1.0 CA D:SER232 4.8 24.8 1.0 CD C:LYS234 4.9 51.2 1.0 C D:SER232 4.9 28.1 1.0 C A:ILE3 4.9 30.6 1.0 CB C:LEU231 4.9 24.7 1.0 O A:PRO2 4.9 33.9 1.0 N C:LEU231 5.0 24.0 1.0 CE C:LYS234 5.0 60.9 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