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Nickel in PDB 3cj2: Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments

Enzymatic activity of Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments

All present enzymatic activity of Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments, PDB code: 3cj2 was solved by C.Kissinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.217, 86.133, 120.270, 90.00, 96.54, 90.00
R / Rfree (%) 21 / 26

Other elements in 3cj2:

The structure of Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments (pdb code 3cj2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments, PDB code: 3cj2:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3cj2

Go back to Nickel Binding Sites List in 3cj2
Nickel binding site 1 out of 2 in the Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni711

b:40.4
occ:1.00
O B:HOH689 2.1 25.8 1.0
OD2 A:ASP66 2.2 22.4 1.0
NE2 B:HIS1 2.2 32.4 1.0
CE1 B:HIS1 2.6 41.9 1.0
CG A:ASP66 3.0 29.3 1.0
OD1 A:ASP66 3.2 19.3 1.0
CD2 B:HIS1 3.4 33.6 1.0
ND1 B:HIS1 3.8 35.4 1.0
O A:HOH819 4.0 22.6 1.0
CG B:HIS1 4.2 37.3 1.0
CB A:ASP66 4.4 16.4 1.0
CB A:ASP62 4.6 11.8 1.0
O A:ASP62 4.6 18.2 1.0
C A:ASP62 5.0 12.9 1.0

Nickel binding site 2 out of 2 in 3cj2

Go back to Nickel Binding Sites List in 3cj2
Nickel binding site 2 out of 2 in the Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Hepatitis C Virus Rna-Dependent Rna Polymerase NS5B in Complex with Optimized Small Molecule Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni727

b:49.1
occ:1.00
OD2 B:ASP66 2.1 21.3 1.0
NE2 A:HIS1 2.2 47.1 1.0
CG B:ASP66 3.0 24.4 1.0
CE1 A:HIS1 3.0 44.4 1.0
CD2 A:HIS1 3.1 35.2 1.0
OD1 B:ASP66 3.3 16.6 1.0
O B:HOH759 3.7 28.3 1.0
ND1 A:HIS1 4.1 35.3 1.0
CG A:HIS1 4.1 38.6 1.0
O B:HOH688 4.1 23.3 1.0
CB B:ASP66 4.4 14.8 1.0
CB B:ASP62 4.7 17.9 1.0
O B:ASP62 4.8 16.3 1.0

Reference:

S.S.Antonysamy, B.Aubol, J.Blaney, M.F.Browner, A.M.Giannetti, S.F.Harris, N.Hebert, J.Hendle, S.Hopkins, E.Jefferson, C.Kissinger, V.Leveque, D.Marciano, E.Mcgee, I.Najera, B.Nolan, M.Tomimoto, E.Torres, T.Wright. Fragment-Based Discovery of Hepatitis C Virus NS5B Rna Polymerase Inhibitors. Bioorg.Med.Chem.Lett. V. 18 2990 2008.
ISSN: ISSN 0960-894X
PubMed: 18400495
DOI: 10.1016/J.BMCL.2008.03.056
Page generated: Wed Dec 16 01:21:51 2020

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