Sodium in PDB 4jmy: Crystal Structure of Hcv NS3/NS4A Protease Complexed with Ddivpc Peptide

All present enzymatic activity of Crystal Structure of Hcv NS3/NS4A Protease Complexed with Ddivpc Peptide:
3.4.21.98;

The structure of Crystal Structure of Hcv NS3/NS4A Protease Complexed with Ddivpc Peptide, PDB code: 4jmy was solved by C.T.Lemke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.24 / 1.95
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	94.123, 94.123, 83.236, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 25.4

The structure of Crystal Structure of Hcv NS3/NS4A Protease Complexed with Ddivpc Peptide also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Hcv NS3/NS4A Protease Complexed with Ddivpc Peptide (pdb code 4jmy). 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 Hcv NS3/NS4A Protease Complexed with Ddivpc Peptide, PDB code: 4jmy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Hcv NS3/NS4A Protease Complexed with Ddivpc Peptide


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 Hcv NS3/NS4A Protease Complexed with Ddivpc Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:40.8 occ:1.00 O A:ALA5 2.5 30.5 1.0 O A:ALA111 2.5 31.3 1.0 O A:HOH340 2.6 41.6 1.0 O A:HOH308 2.7 33.9 1.0 O A:HOH342 2.8 42.6 1.0 O A:HOH336 2.9 41.4 1.0 C A:ALA111 3.5 35.0 1.0 C A:ALA5 3.5 32.1 1.0 CB A:ALA111 4.0 33.2 1.0 N A:ALA5 4.1 36.0 1.0 O A:HOH371 4.1 47.0 1.0 O A:HOH306 4.3 33.0 1.0 CA A:ALA5 4.3 34.3 1.0 N A:ASP112 4.4 33.0 1.0 CA A:ALA111 4.4 30.3 1.0 CA A:ASP112 4.4 31.7 1.0 CB A:ALA5 4.5 30.7 1.0 N A:TYR6 4.5 30.7 1.0 OD1 A:ASP112 4.6 44.8 1.0 CA A:TYR6 4.6 32.0 1.0 O A:HOH386 4.7 49.1 1.0 O A:HOH316 4.8 38.0 1.0 O A:HIS110 4.8 38.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Hcv NS3/NS4A Protease Complexed with Ddivpc Peptide


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 Hcv NS3/NS4A Protease Complexed with Ddivpc Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:49.7 occ:1.00 O B:ALA5 2.6 34.4 1.0 O B:ALA111 2.6 31.7 1.0 O B:HOH361 2.8 49.5 1.0 O B:HOH308 2.9 36.2 1.0 O B:HOH379 3.0 54.1 1.0 C B:ALA111 3.6 34.3 1.0 C B:ALA5 3.7 35.0 1.0 O B:HOH355 3.8 47.8 1.0 CB B:ALA111 4.1 36.4 1.0 N B:ALA5 4.4 36.1 1.0 O B:HOH339 4.4 45.0 1.0 N B:ASP112 4.5 35.4 1.0 CA B:ALA5 4.5 36.4 1.0 CA B:ALA111 4.5 35.1 1.0 CA B:ASP112 4.5 35.2 1.0 O B:HOH319 4.6 41.0 1.0 OD2 B:ASP112 4.6 44.8 1.0 N B:TYR6 4.6 33.6 1.0 CA B:TYR6 4.7 36.0 1.0 CB B:ALA5 4.8 29.9 1.0 O B:HIS110 4.8 42.1 1.0

S.Laplante, C.T.Lemke. Importance of the Peptide Scaffold of Drugs That Target the Hepatitis C Virus NS3 Protease and Its Crucial Bioactive Conformation and Dynamic Factors. To Be Published.