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Chlorine in PDB 3vqs: Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor

Protein crystallography data

The structure of Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor, PDB code: 3vqs was solved by T.Adachi, S.Doi, I.Ando, K.Sugimoto, T.Orita, A.Nomura, M.Kamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.97 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.120, 101.180, 250.060, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.4

Other elements in 3vqs:

The structure of Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor also contains other interesting chemical elements:

Fluorine (F) 28 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor (pdb code 3vqs). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor, PDB code: 3vqs:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3vqs

Go back to Chlorine Binding Sites List in 3vqs
Chlorine binding site 1 out of 2 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:43.8
occ:1.00
NE B:ARG168 3.1 27.9 1.0
O B:HOH3116 3.1 38.0 1.0
OG B:SER96 3.4 38.1 1.0
CB B:SER96 3.6 43.1 1.0
CD B:PRO93 3.6 37.8 1.0
NZ B:LYS172 3.8 28.4 1.0
NH2 B:ARG168 3.9 28.6 1.0
CD B:ARG168 3.9 28.1 1.0
CZ B:ARG168 3.9 29.3 1.0
CG2 B:THR92 3.9 34.7 1.0
CB B:ARG168 3.9 26.1 1.0
CD1 B:LEU165 4.2 24.4 1.0
CG B:PRO93 4.2 41.5 1.0
CG B:ARG168 4.5 27.0 1.0
N B:PRO93 4.7 37.0 1.0
O B:HOH3191 4.7 46.8 1.0
CB B:THR92 4.7 33.5 1.0
OG1 B:THR92 4.8 37.0 1.0
CA B:THR92 4.8 33.2 1.0
O B:HOH3005 4.9 25.2 1.0

Chlorine binding site 2 out of 2 in 3vqs

Go back to Chlorine Binding Sites List in 3vqs
Chlorine binding site 2 out of 2 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl602

b:47.9
occ:1.00
OG C:SER96 3.1 46.4 1.0
NE C:ARG168 3.2 32.2 1.0
O C:HOH3230 3.2 47.7 1.0
CD C:PRO93 3.6 44.0 1.0
CB C:SER96 3.7 48.7 1.0
CG2 C:THR92 3.7 39.0 1.0
NZ C:LYS172 3.8 38.0 1.0
NH2 C:ARG168 3.9 31.1 1.0
CZ C:ARG168 4.0 33.8 1.0
CB C:ARG168 4.0 31.3 1.0
CD C:ARG168 4.0 32.6 1.0
CD1 C:LEU165 4.2 29.1 1.0
CG C:PRO93 4.3 44.4 1.0
CG C:ARG168 4.6 31.0 1.0
N C:PRO93 4.7 44.0 1.0
CB C:THR92 4.7 36.9 1.0
OG1 C:THR92 4.8 37.6 1.0
CA C:THR92 4.8 41.0 1.0

Reference:

I.Ando, T.Adachi, N.Ogura, Y.Toyonaga, K.Sugimoto, H.Abe, M.Kamada, T.Noguchi. Preclinical Characterization of Jtk-853, A Novel Nonnucleoside Inhibitor of the Hepatitis C Virus Rna-Dependent Rna Polymerase. Antimicrob.Agents Chemother. V. 56 4250 2012.
ISSN: ISSN 0066-4804
PubMed: 22615294
DOI: 10.1128/AAC.00312-12
Page generated: Sat Dec 12 10:18:09 2020

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