Zinc in PDB 5i3p: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 27

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 27, PDB code: 5i3p 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)	31.48 / 2.45
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.364, 176.111, 57.913, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 22.1

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 27 (pdb code 5i3p). 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 27, PDB code: 5i3p:
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 27


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 27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:53.5 occ:1.00 NE2 A:HIS712 2.0 42.8 1.0 SG A:CYS728 2.3 43.5 1.0 NE2 A:HIS714 2.3 46.8 1.0 SG A:CYS847 2.3 53.6 1.0 CB A:CYS728 2.9 38.1 1.0 CD2 A:HIS712 3.0 43.0 1.0 CE1 A:HIS712 3.1 42.4 1.0 CD2 A:HIS714 3.3 46.8 1.0 CE1 A:HIS714 3.3 46.6 1.0 CB A:CYS847 3.3 48.7 1.0 CG A:HIS712 4.1 39.5 1.0 ND1 A:HIS712 4.2 42.3 1.0 CA A:CYS728 4.2 36.1 1.0 CD1 A:LEU839 4.3 39.7 1.0 CG A:HIS714 4.4 44.1 1.0 ND1 A:HIS714 4.5 46.9 1.0 C A:CYS728 4.5 38.6 1.0 O A:HOH1372 4.6 68.8 1.0 CA A:CYS847 4.7 47.1 1.0 N A:ARG729 4.8 33.1 1.0 O A:GLU843 4.9 46.2 1.0 O A:HOH1375 4.9 53.8 1.0 O A:CYS728 5.0 41.0 1.0 NH2 A:ARG769 5.0 32.8 1.0

Zinc binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 27


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 27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:48.0 occ:1.00 NE2 A:HIS441 2.1 45.0 1.0 OE1 A:GLU437 2.2 53.3 1.0 SG A:CYS446 2.3 48.3 1.0 SG A:CYS449 2.4 55.1 1.0 CE1 A:HIS441 2.9 44.8 1.0 CB A:CYS449 3.1 51.8 1.0 CD2 A:HIS441 3.2 44.7 1.0 CD A:GLU437 3.2 57.6 1.0 CB A:CYS446 3.4 44.8 1.0 N A:CYS449 3.6 53.6 1.0 CG A:GLU437 3.6 48.7 1.0 CA A:CYS446 3.8 45.0 1.0 CA A:CYS449 4.0 52.1 1.0 ND1 A:HIS441 4.1 45.2 1.0 OE2 A:GLU437 4.2 51.2 1.0 CG A:HIS441 4.2 43.2 1.0 N A:GLY447 4.2 46.2 1.0 N A:SER448 4.4 50.9 1.0 C A:CYS446 4.5 49.0 1.0 C A:SER448 4.6 58.0 1.0 CG2 A:THR571 4.7 46.4 1.0 O A:HOH1136 4.8 48.9 1.0 O A:LYS445 4.9 47.5 1.0 CD1 A:LEU483 5.0 44.9 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