Zinc in PDB 5i3q: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 29

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 29, PDB code: 5i3q 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)	27.53 / 1.88
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.136, 175.903, 57.789, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.2

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 29 (pdb code 5i3q). 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 29, PDB code: 5i3q:
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 29


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 29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:25.3 occ:1.00 NE2 A:HIS712 2.1 23.5 1.0 NE2 A:HIS714 2.1 27.2 1.0 SG A:CYS847 2.2 28.9 1.0 SG A:CYS728 2.4 24.7 1.0 CD2 A:HIS712 3.1 24.1 1.0 CD2 A:HIS714 3.1 25.7 1.0 CE1 A:HIS712 3.1 23.2 1.0 CB A:CYS728 3.1 21.1 1.0 CE1 A:HIS714 3.1 27.6 1.0 CB A:CYS847 3.2 25.1 1.0 CG A:HIS712 4.2 23.3 1.0 CG A:HIS714 4.2 26.1 1.0 ND1 A:HIS712 4.2 24.2 1.0 ND1 A:HIS714 4.3 28.4 1.0 CD1 A:LEU839 4.3 25.3 1.0 CA A:CYS728 4.4 21.8 1.0 O A:HOH1482 4.4 32.0 1.0 O A:HOH1520 4.6 36.3 1.0 C A:CYS728 4.6 25.9 1.0 CA A:CYS847 4.6 25.3 1.0 O A:HOH1582 4.7 51.0 1.0 N A:ARG729 4.7 23.4 1.0 NH2 A:ARG769 4.8 25.5 1.0 O A:HOH1214 4.9 38.5 1.0

Zinc binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 29


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 29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:34.7 occ:1.00 NE2 A:HIS441 2.1 35.0 1.0 OE1 A:GLU437 2.1 43.8 1.0 SG A:CYS449 2.2 37.4 1.0 SG A:CYS446 2.3 35.5 1.0 CE1 A:HIS441 3.1 35.0 1.0 CD2 A:HIS441 3.1 34.5 1.0 CD A:GLU437 3.1 39.4 1.0 CB A:CYS449 3.2 34.5 1.0 CB A:CYS446 3.4 31.9 1.0 CG A:GLU437 3.5 36.0 1.0 N A:CYS449 3.7 37.6 1.0 CA A:CYS446 3.7 33.2 1.0 CA A:CYS449 4.0 35.4 1.0 N A:GLY447 4.1 37.6 1.0 CG A:HIS441 4.2 33.9 1.0 ND1 A:HIS441 4.2 35.4 1.0 OE2 A:GLU437 4.3 40.9 1.0 N A:SER448 4.4 40.2 1.0 C A:CYS446 4.4 40.5 1.0 C A:SER448 4.6 42.3 1.0 O A:HOH1230 4.7 40.9 1.0 CG2 A:THR571 4.8 38.0 1.0 O A:HOH1168 4.9 47.7 1.0 O A:LYS445 4.9 37.5 1.0 CB A:GLU437 5.0 34.1 1.0

S.P.Lim, C.G.Noble, C.C.Seh, T.S.Soh, A.El Sahili, G.K.Chan, J.Lescar, R.Arora, T.Benson, S.Nilar, U.Manjunatha, K.F.Wan, H.Dong, X.Xie, P.Y.Shi, F.Yokokawa. Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling Plos Pathog. V. 12 05737 2016.
ISSN: ESSN 1553-7374
PubMed: 27500641
DOI: 10.1371/JOURNAL.PPAT.1005737