Zinc 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:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-107, PDB code: 3vws:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn1001 b:49.3 occ:1.00 NE2 A:HIS714 2.1 43.6 1.0 NE2 A:HIS712 2.2 43.8 1.0 SG A:CYS728 2.4 38.8 1.0 SG A:CYS847 2.6 49.4 1.0 CD2 A:HIS712 2.8 43.5 1.0 CB A:CYS728 3.0 34.3 1.0 CE1 A:HIS714 3.1 43.3 1.0 CD2 A:HIS714 3.1 43.3 1.0 CE1 A:HIS712 3.4 43.3 1.0 CB A:CYS847 3.4 45.4 1.0 CG A:HIS712 4.1 40.0 1.0 CD1 A:LEU839 4.1 45.0 1.0 CG A:HIS714 4.3 40.2 1.0 ND1 A:HIS714 4.3 42.9 1.0 CA A:CYS728 4.3 33.6 1.0 ND1 A:HIS712 4.4 43.2 1.0 C A:CYS728 4.5 37.2 1.0 O A:HOH1264 4.7 53.6 1.0 O A:HOH1458 4.7 54.6 1.0 N A:ARG729 4.8 34.4 1.0 NH2 A:ARG769 4.8 32.8 1.0 O A:GLU843 4.9 48.2 1.0 CA A:CYS847 4.9 44.8 1.0 O A:CYS728 5.0 36.7 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1002 b:39.1 occ:1.00 NE2 A:HIS441 2.0 39.3 1.0 SG A:CYS449 2.2 41.1 1.0 SG A:CYS446 2.3 40.0 1.0 OE1 A:GLU437 2.3 50.1 1.0 CE1 A:HIS441 2.9 39.3 1.0 CD A:GLU437 3.1 51.3 1.0 CB A:CYS449 3.1 38.3 1.0 CD2 A:HIS441 3.2 39.6 1.0 CG A:GLU437 3.3 37.4 1.0 CB A:CYS446 3.4 36.7 1.0 N A:CYS449 3.6 41.1 1.0 CA A:CYS446 3.8 37.6 1.0 CA A:CYS449 3.9 39.3 1.0 ND1 A:HIS441 4.1 40.0 1.0 OE2 A:GLU437 4.1 49.2 1.0 N A:GLY447 4.2 40.3 1.0 CG A:HIS441 4.2 38.4 1.0 N A:SER448 4.4 41.5 1.0 C A:CYS446 4.4 43.0 1.0 C A:SER448 4.6 45.2 1.0 CG2 A:THR571 4.6 51.3 1.0 O A:HOH1156 4.6 43.5 1.0 O A:HOH1292 4.8 51.8 1.0 CB A:GLU437 4.8 34.0 1.0 O A:LYS445 4.9 40.5 1.0 CD1 A:LEU483 5.0 34.5 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