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Chlorine in PDB 3gol: Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D

Enzymatic activity of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D

All present enzymatic activity of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D:
2.7.7.48;

Protein crystallography data

The structure of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D, PDB code: 3gol was solved by O.Nyanguile, H.De Bondt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.81 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.048, 106.620, 134.679, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 25

Other elements in 3gol:

The structure of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D (pdb code 3gol). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D, PDB code: 3gol:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3gol

Go back to Chlorine Binding Sites List in 3gol
Chlorine binding site 1 out of 4 in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl579

b:38.4
occ:1.00
 CL29 A:XND579 0.0 38.4 1.0
C22 A:XND579 1.7 40.0 1.0
C23 A:XND579 2.7 37.9 1.0
C21 A:XND579 2.7 33.9 1.0
CD A:ARG200 3.6 32.5 1.0
CD1 A:LEU384 3.6 42.6 1.0
CB A:CYS366 3.6 39.0 1.0
NE A:ARG200 3.7 34.3 1.0
NH1 A:ARG200 3.9 37.2 1.0
CZ A:ARG200 3.9 36.2 1.0
C24 A:XND579 4.0 37.1 1.0
C20 A:XND579 4.0 37.0 1.0
OG A:SER368 4.1 37.1 1.0
O A:CYS366 4.3 37.6 1.0
CB A:SER368 4.4 35.7 1.0
O A:HOH600 4.5 3.5 1.0
C16 A:XND579 4.5 33.3 1.0
O A:SER365 4.5 38.1 1.0
SG A:CYS366 4.6 46.8 1.0
NH2 A:ARG200 4.7 38.4 1.0
CA A:CYS366 4.8 37.4 1.0
C A:CYS366 4.9 36.7 1.0
CG A:LEU384 4.9 38.9 1.0

Chlorine binding site 2 out of 4 in 3gol

Go back to Chlorine Binding Sites List in 3gol
Chlorine binding site 2 out of 4 in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl579

b:47.9
occ:1.00
 CL28 A:XND579 0.0 47.9 1.0
C20 A:XND579 1.7 37.0 1.0
C16 A:XND579 2.7 33.3 1.0
C21 A:XND579 2.7 33.9 1.0
N10 A:XND579 2.8 28.7 1.0
C11 A:XND579 3.0 33.4 1.0
CE1 A:PHE193 3.4 25.4 1.0
C15 A:XND579 3.4 22.1 1.0
C9 A:XND579 3.4 24.3 1.0
C17 A:XND579 3.5 33.5 1.0
CD1 A:TYR448 3.6 36.5 1.0
CE1 A:TYR448 3.7 33.6 1.0
O18 A:XND579 3.8 28.2 1.0
C22 A:XND579 4.0 40.0 1.0
C24 A:XND579 4.0 37.1 1.0
OD1 A:ASN316 4.0 38.4 1.0
CD1 A:PHE193 4.0 29.3 1.0
CZ A:PHE193 4.2 25.6 1.0
SG A:CYS366 4.4 46.8 1.0
CG A:TYR448 4.4 37.2 1.0
C23 A:XND579 4.5 37.9 1.0
C5 A:XND579 4.5 20.3 1.0
C14 A:XND579 4.5 20.8 1.0
CG A:ASN316 4.5 32.0 1.0
CB A:ASN316 4.5 30.1 1.0
C19 A:XND579 4.6 28.1 1.0
CZ A:TYR448 4.7 36.1 1.0
C8 A:XND579 4.7 21.2 1.0
CA A:TYR448 4.7 36.9 1.0
CB A:TYR448 5.0 37.5 1.0
O25 A:XND579 5.0 22.8 1.0

Chlorine binding site 3 out of 4 in 3gol

Go back to Chlorine Binding Sites List in 3gol
Chlorine binding site 3 out of 4 in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl579

b:53.5
occ:1.00
 CL29 B:XND579 0.0 53.5 1.0
C22 B:XND579 1.7 49.3 1.0
C21 B:XND579 2.6 49.4 1.0
C23 B:XND579 2.7 49.1 1.0
CB B:CYS366 3.6 44.3 1.0
NE B:ARG200 3.8 31.1 1.0
CZ B:ARG200 3.9 33.1 1.0
CD B:ARG200 3.9 28.5 1.0
C20 B:XND579 3.9 52.8 1.0
NH1 B:ARG200 4.0 39.5 1.0
C24 B:XND579 4.0 50.7 1.0
CD1 B:LEU384 4.0 34.5 1.0
OG B:SER368 4.1 41.9 1.0
O B:CYS366 4.2 41.3 1.0
O B:SER365 4.3 45.4 1.0
CB B:SER368 4.3 38.6 1.0
SG B:CYS366 4.4 44.0 1.0
NH2 B:ARG200 4.5 32.1 1.0
C16 B:XND579 4.5 50.5 1.0
CG B:LEU384 4.6 33.0 1.0
CA B:CYS366 4.8 42.9 1.0
C B:CYS366 4.9 42.4 1.0
CD2 B:LEU384 5.0 35.1 1.0

Chlorine binding site 4 out of 4 in 3gol

Go back to Chlorine Binding Sites List in 3gol
Chlorine binding site 4 out of 4 in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor (R)- 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl579

b:56.1
occ:1.00
 CL28 B:XND579 0.0 56.1 1.0
C20 B:XND579 1.7 52.8 1.0
C21 B:XND579 2.6 49.4 1.0
C16 B:XND579 2.7 50.5 1.0
N10 B:XND579 3.0 41.3 1.0
C11 B:XND579 3.0 47.6 1.0
C15 B:XND579 3.3 32.2 1.0
CE1 B:PHE193 3.3 28.4 1.0
CD1 B:TYR448 3.5 36.7 1.0
C9 B:XND579 3.5 36.6 1.0
CE1 B:TYR448 3.6 35.4 1.0
C17 B:XND579 3.8 51.5 1.0
C22 B:XND579 3.9 49.3 1.0
C24 B:XND579 4.0 50.7 1.0
OD1 B:ASN316 4.1 38.4 1.0
CD1 B:PHE193 4.1 30.3 1.0
CZ B:PHE193 4.1 30.9 1.0
O18 B:XND579 4.2 49.3 1.0
CG B:TYR448 4.3 37.4 1.0
C14 B:XND579 4.4 39.0 1.0
C23 B:XND579 4.4 49.1 1.0
SG B:CYS366 4.5 44.0 1.0
CZ B:TYR448 4.5 34.5 1.0
C5 B:XND579 4.6 41.1 1.0
CG B:ASN316 4.7 35.9 1.0
C8 B:XND579 4.7 34.0 1.0
CA B:TYR448 4.7 35.7 1.0
CB B:ASN316 4.7 32.9 1.0
C19 B:XND579 4.9 51.6 1.0
CB B:TYR448 4.9 35.5 1.0

Reference:

D.Mcgowan, O.Nyanguile, M.D.Cummings, S.Vendeville, K.Vandyck, W.Van Den Broeck, C.W.Boutton, H.De Bondt, L.Quirynen, K.Amssoms, J.F.Bonfanti, S.Last, K.Rombauts, A.Tahri, L.Hu, F.Delouvroy, K.Vermeiren, G.Vandercruyssen, L.Van Der Helm, E.Cleiren, W.Mostmans, P.Lory, G.Pille, K.Van Emelen, G.Fanning, F.Pauwels, T.I.Lin, K.Simmen, P.Raboisson. 1,5-Benzodiazepine Inhibitors of Hcv NS5B Polymerase. Bioorg.Med.Chem.Lett. V. 19 2492 2009.
ISSN: ISSN 0960-894X
PubMed: 19342234
DOI: 10.1016/J.BMCL.2009.03.035
Page generated: Fri Jul 11 05:44:22 2025

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