Zinc in PDB 5hmz: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 23

All present enzymatic activity of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 23:
2.7.7.48;

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 23, PDB code: 5hmz 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)	39.80 / 1.99
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	160.875, 175.498, 57.870, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.1

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 23 (pdb code 5hmz). 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 23, PDB code: 5hmz:
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 23


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 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:29.1 occ:1.00 NE2 A:HIS712 2.1 27.0 1.0 NE2 A:HIS714 2.1 30.3 1.0 SG A:CYS847 2.3 30.6 1.0 SG A:CYS728 2.3 29.2 1.0 CE1 A:HIS712 3.0 26.7 1.0 CE1 A:HIS714 3.0 30.2 1.0 CB A:CYS728 3.1 25.4 1.0 CD2 A:HIS712 3.1 27.7 1.0 CD2 A:HIS714 3.1 29.8 1.0 CB A:CYS847 3.3 27.0 1.0 ND1 A:HIS712 4.2 28.9 1.0 ND1 A:HIS714 4.2 30.5 1.0 CG A:HIS712 4.2 26.9 1.0 CG A:HIS714 4.2 28.5 1.0 CD1 A:LEU839 4.3 30.9 1.0 CA A:CYS728 4.4 25.4 1.0 O A:HOH1405 4.4 33.1 1.0 O A:HOH1457 4.4 42.2 1.0 C A:CYS728 4.6 29.6 1.0 NH2 A:ARG769 4.6 29.6 1.0 CA A:CYS847 4.7 27.5 1.0 N A:ARG729 4.7 27.3 1.0 O A:HOH1510 4.8 53.6 1.0 O A:HOH1140 5.0 37.7 1.0

Zinc binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 23


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 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:37.5 occ:1.00 NE2 A:HIS441 2.1 38.1 1.0 OE1 A:GLU437 2.2 47.9 1.0 SG A:CYS449 2.2 38.4 1.0 SG A:CYS446 2.3 37.6 1.0 CE1 A:HIS441 3.1 37.9 1.0 CD A:GLU437 3.1 49.3 1.0 CB A:CYS449 3.1 35.9 1.0 CD2 A:HIS441 3.1 38.0 1.0 CG A:GLU437 3.4 36.3 1.0 CB A:CYS446 3.5 34.4 1.0 N A:CYS449 3.6 38.7 1.0 CA A:CYS446 3.8 35.8 1.0 CA A:CYS449 4.0 36.9 1.0 N A:GLY447 4.1 39.5 1.0 OE2 A:GLU437 4.2 48.4 1.0 ND1 A:HIS441 4.2 38.5 1.0 CG A:HIS441 4.2 37.0 1.0 N A:SER448 4.3 40.1 1.0 C A:CYS446 4.5 42.9 1.0 C A:SER448 4.5 43.5 1.0 O A:HOH1180 4.7 41.2 1.0 CG2 A:THR571 4.9 42.4 1.0 O A:LYS445 4.9 39.9 1.0 CB A:GLU437 4.9 35.5 1.0 CA A:SER448 5.0 40.3 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