Zinc in PDB 5jjs: Dengue 3 NS5 Protein with Compound 27

The structure of Dengue 3 NS5 Protein with Compound 27, PDB code: 5jjs was solved by J.Lescar, A.El Sahili, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.16 / 1.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.690, 150.230, 68.520, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.8

The structure of Dengue 3 NS5 Protein with Compound 27 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Dengue 3 NS5 Protein with Compound 27 (pdb code 5jjs). 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 3 NS5 Protein with Compound 27, PDB code: 5jjs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Dengue 3 NS5 Protein with 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 3 NS5 Protein with Compound 27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:14.8 occ:0.75 OE2 A:GLU437 2.0 19.8 1.0 NE2 A:HIS441 2.1 18.5 1.0 SG A:CYS449 2.2 22.7 1.0 SG A:CYS446 2.3 20.4 1.0 CE1 A:HIS441 3.0 18.3 1.0 CD A:GLU437 3.1 18.9 1.0 CD2 A:HIS441 3.1 18.8 1.0 CB A:CYS449 3.1 20.2 1.0 CB A:CYS446 3.3 16.0 1.0 CG A:GLU437 3.4 20.5 1.0 CA A:CYS446 3.7 16.6 1.0 N A:CYS449 3.7 23.9 1.0 CA A:CYS449 4.0 21.5 1.0 N A:GLY447 4.1 19.9 1.0 OE1 A:GLU437 4.2 23.7 1.0 ND1 A:HIS441 4.2 19.1 1.0 CG A:HIS441 4.2 17.9 1.0 C A:CYS446 4.3 21.6 1.0 N A:SER448 4.3 24.0 1.0 CG2 A:THR571 4.5 25.6 1.0 O A:HOH1549 4.6 23.8 1.0 C A:SER448 4.6 28.6 1.0 O A:HOH1312 4.8 32.6 1.0 CD1 A:LEU483 4.9 20.0 1.0 CB A:GLU437 5.0 19.1 1.0 O A:LYS445 5.0 19.8 1.0

Zinc binding site 2 out of 2 in the Dengue 3 NS5 Protein with 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 3 NS5 Protein with Compound 27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:17.5 occ:0.75 NE2 A:HIS712 2.0 20.5 1.0 CE1 A:HIS714 2.1 23.2 1.0 SG A:CYS847 2.3 25.9 1.0 SG A:CYS728 2.4 20.3 1.0 NE2 A:HIS714 2.9 24.7 1.0 CE1 A:HIS712 3.0 21.2 1.0 CD2 A:HIS712 3.0 20.8 1.0 ND1 A:HIS714 3.1 24.0 1.0 CB A:CYS728 3.2 16.0 1.0 CB A:CYS847 3.3 22.1 1.0 CD2 A:HIS714 4.1 24.4 1.0 CG A:HIS712 4.2 21.0 1.0 ND1 A:HIS712 4.2 21.9 1.0 CG A:HIS714 4.2 21.5 1.0 CD1 A:LEU839 4.3 23.6 1.0 O A:HOH1670 4.3 36.1 1.0 O2 A:EDO1018 4.4 53.9 1.0 CA A:CYS728 4.4 15.2 1.0 O A:HOH1494 4.5 27.2 1.0 C A:CYS728 4.6 21.0 1.0 CA A:CYS847 4.7 22.1 1.0 N A:ARG729 4.7 18.0 1.0 NH1 A:ARG769 4.7 22.5 1.0 O A:HOH1116 4.9 35.7 1.0 O1 A:EDO1018 4.9 56.0 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