Zinc in PDB 5hmw: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 5

All present enzymatic activity of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 5:
2.7.7.48;

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 5, PDB code: 5hmw was solved by C.G.Noble, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.00 / 2.15
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.880, 179.390, 58.000, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.2

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 5 (pdb code 5hmw). 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 Compound 5, PDB code: 5hmw:
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 Compound 5


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 Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:30.4 occ:1.00 NE2 A:HIS712 1.9 29.1 1.0 NE2 A:HIS714 2.0 26.8 1.0 SG A:CYS728 2.2 29.7 1.0 SG A:CYS847 2.3 36.6 1.0 CE1 A:HIS712 2.8 29.1 1.0 CD2 A:HIS714 3.0 26.6 1.0 CD2 A:HIS712 3.1 28.6 1.0 CE1 A:HIS714 3.1 26.9 1.0 CB A:CYS728 3.1 26.2 1.0 CB A:CYS847 3.4 32.7 1.0 ND1 A:HIS712 4.0 29.9 1.0 CG A:HIS712 4.1 28.3 1.0 CG A:HIS714 4.2 27.4 1.0 ND1 A:HIS714 4.2 28.2 1.0 CD1 A:LEU839 4.2 33.9 1.0 O A:HOH1306 4.3 37.9 1.0 CA A:CYS728 4.4 26.6 1.0 C A:CYS728 4.5 30.6 1.0 N A:ARG729 4.5 27.9 1.0 O A:HOH1344 4.7 45.8 1.0 CA A:CYS847 4.8 31.4 1.0 NH2 A:ARG769 4.9 19.4 1.0 O A:ARG729 4.9 34.1 1.0 O A:GLU843 4.9 34.5 1.0

Zinc binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 5


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 Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:48.7 occ:1.00 NE2 A:HIS441 2.1 43.8 1.0 SG A:CYS449 2.2 49.0 1.0 OE1 A:GLU437 2.3 56.9 1.0 SG A:CYS446 2.4 46.6 1.0 CE1 A:HIS441 2.9 43.3 1.0 CB A:CYS449 3.1 45.9 1.0 CD A:GLU437 3.2 58.3 1.0 CD2 A:HIS441 3.2 44.2 1.0 CG A:GLU437 3.4 49.1 1.0 CB A:CYS446 3.5 42.7 1.0 N A:CYS449 3.7 48.0 1.0 CA A:CYS446 3.8 43.0 1.0 CA A:CYS449 4.0 46.9 1.0 ND1 A:HIS441 4.1 44.0 1.0 N A:GLY447 4.2 45.2 1.0 CG A:HIS441 4.3 42.7 1.0 OE2 A:GLU437 4.3 53.6 1.0 N A:SER448 4.4 48.5 1.0 C A:CYS446 4.5 49.0 1.0 O A:HOH1115 4.7 38.7 1.0 C A:SER448 4.7 52.1 1.0 CG2 A:THR571 4.9 47.8 1.0 CB A:GLU437 4.9 43.6 1.0 O A:LYS445 4.9 44.8 1.0

F.Yokokawa, S.Nilar, C.G.Noble, S.P.Lim, R.Rao, S.Tania, G.Wang, G.Lee, J.Hunziker, R.Karuna, U.Manjunatha, P.Y.Shi, P.W.Smith. Discovery of Potent Non-Nucleoside Inhibitors of Dengue Viral Rna-Dependent Rna Polymerase From A Fragment Hit Using Structure-Based Drug Design J.Med.Chem. V. 59 3935 2016.
ISSN: ISSN 0022-2623
PubMed: 26984786
DOI: 10.1021/ACS.JMEDCHEM.6B00143