Chlorine in PDB 3vws: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107

All present enzymatic activity of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107:
2.7.7.48;

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107, PDB code: 3vws was solved by C.G.Noble, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.460, 177.730, 57.930, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.4

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Chlorine atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107 (pdb code 3vws). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107, PDB code: 3vws:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1003 b:85.2 occ:1.00 CL1 A:VWS1003 0.0 85.2 1.0 C5 A:VWS1003 1.8 85.0 1.0 C4 A:VWS1003 2.6 85.3 1.0 C6 A:VWS1003 2.8 85.3 1.0 CD1 A:PHE485 3.4 31.2 1.0 CG A:PHE485 3.9 31.8 1.0 C3 A:VWS1003 4.0 86.2 1.0 CB A:PHE485 4.0 31.5 1.0 CE1 A:PHE485 4.1 30.6 1.0 C2 A:VWS1003 4.1 86.1 1.0 CE1 A:PHE398 4.2 42.9 1.0 O A:HOH1420 4.2 51.1 1.0 CG2 A:VAL603 4.3 46.8 1.0 CG1 A:VAL603 4.3 45.3 1.0 CD1 A:PHE398 4.4 42.2 1.0 C4 A:VWS1004 4.5 70.3 1.0 C1 A:VWS1003 4.6 87.0 1.0 CE A:LYS401 4.6 70.9 1.0 CD A:LYS401 4.8 65.7 1.0 C3 A:VWS1004 4.9 74.7 1.0 CD2 A:PHE485 4.9 32.1 1.0 CB A:VAL603 5.0 46.8 1.0

Chlorine binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1004 b:62.0 occ:1.00 CL1 A:VWS1004 0.0 62.0 1.0 C5 A:VWS1004 1.8 68.4 1.0 C4 A:VWS1004 2.7 70.3 1.0 C6 A:VWS1004 2.9 72.4 1.0 CG A:ARG481 3.5 53.2 1.0 C13 A:VWS1003 3.6 67.6 1.0 CE1 A:PHE412 3.6 69.1 1.0 C15 A:VWS1003 3.7 65.0 1.0 CD1 A:PHE412 3.7 68.8 1.0 C10 A:VWS1003 3.7 71.0 1.0 O4 A:VWS1003 4.0 64.2 1.0 O A:GLY601 4.0 58.2 1.0 C3 A:VWS1004 4.0 74.7 1.0 CD A:ARG481 4.1 49.6 1.0 C14 A:VWS1003 4.1 67.5 1.0 C11 A:VWS1003 4.1 74.1 1.0 O5 A:VWS1003 4.1 63.6 1.0 C2 A:VWS1004 4.2 75.6 1.0 CG2 A:VAL603 4.2 46.8 1.0 C9 A:VWS1003 4.3 70.4 1.0 CH2 A:TRP477 4.3 49.7 1.0 O3 A:VWS1003 4.5 68.9 1.0 CZ2 A:TRP477 4.6 50.0 1.0 C1 A:VWS1004 4.7 79.3 1.0 CB A:ARG481 4.7 38.7 1.0 O A:HOH1287 4.7 60.7 1.0 CZ A:PHE412 4.9 67.6 1.0 C16 A:VWS1003 4.9 67.4 1.0

C.G.Noble, S.P.Lim, Y.L.Chen, C.W.Liew, L.Yap, J.Lescar, P.-Y.Shi. Conformational Flexibility of the Dengue Virus Rna-Dependent Rna Polymerase Revealed By A Complex with An Inhibitor J.Virol. V. 87 5291 2013.
ISSN: ISSN 0022-538X
PubMed: 23408636
DOI: 10.1128/JVI.00045-13