Zinc in PDB 5hmy: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 15

All present enzymatic activity of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 15:
2.7.7.48;

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 15, PDB code: 5hmy 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)	21.17 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	160.880, 177.110, 58.070, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.3

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 15 (pdb code 5hmy). 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 15, PDB code: 5hmy:
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 15


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 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:23.2 occ:1.00 NE2 A:HIS712 2.0 22.3 1.0 NE2 A:HIS714 2.1 24.0 1.0 SG A:CYS847 2.3 27.4 1.0 SG A:CYS728 2.3 23.2 1.0 CD2 A:HIS712 3.0 22.2 1.0 CE1 A:HIS714 3.0 23.8 1.0 CE1 A:HIS712 3.1 22.1 1.0 CB A:CYS728 3.1 20.0 1.0 CD2 A:HIS714 3.2 23.7 1.0 CB A:CYS847 3.2 23.6 1.0 CG A:HIS712 4.1 20.8 1.0 ND1 A:HIS712 4.2 22.5 1.0 ND1 A:HIS714 4.2 23.6 1.0 CG A:HIS714 4.2 22.1 1.0 CD1 A:LEU839 4.3 26.2 1.0 O A:HOH1369 4.4 31.0 1.0 CA A:CYS728 4.4 20.1 1.0 C A:CYS728 4.5 24.8 1.0 N A:ARG729 4.6 22.9 1.0 CA A:CYS847 4.6 23.0 1.0 NH2 A:ARG769 4.8 20.0 1.0 O A:HOH1393 4.8 40.6 1.0 O A:ARG729 5.0 28.1 1.0

Zinc binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 15


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 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:36.5 occ:1.00 NE2 A:HIS441 2.1 32.3 1.0 SG A:CYS449 2.2 39.8 1.0 SG A:CYS446 2.3 35.5 1.0 OE1 A:GLU437 2.4 45.6 1.0 CE1 A:HIS441 2.9 32.0 1.0 CB A:CYS449 3.0 37.0 1.0 CD A:GLU437 3.1 46.6 1.0 CD2 A:HIS441 3.2 32.3 1.0 CG A:GLU437 3.3 37.9 1.0 CB A:CYS446 3.5 31.9 1.0 N A:CYS449 3.6 38.1 1.0 CA A:CYS449 3.9 37.6 1.0 CA A:CYS446 3.9 32.2 1.0 OE2 A:GLU437 4.1 54.9 1.0 ND1 A:HIS441 4.1 32.8 1.0 CG A:HIS441 4.2 31.7 1.0 N A:GLY447 4.3 36.1 1.0 N A:SER448 4.4 37.9 1.0 C A:CYS446 4.6 38.5 1.0 O A:HOH1181 4.6 39.5 1.0 C A:SER448 4.6 42.5 1.0 CG2 A:THR571 4.8 33.4 1.0 CB A:GLU437 4.9 32.3 1.0 O A:LYS445 4.9 35.5 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