Zinc in PDB 5f3t: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Jf-31-MG46

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Jf-31-MG46, PDB code: 5f3t 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)	40.40 / 2.05
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.580, 177.090, 57.880, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Jf-31-MG46 (pdb code 5f3t). 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 Jf-31-MG46, PDB code: 5f3t:
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 Jf-31-MG46


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 Jf-31-MG46 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:25.9 occ:1.00 NE2 A:HIS714 2.0 25.0 1.0 NE2 A:HIS712 2.1 24.8 1.0 SG A:CYS847 2.2 27.1 1.0 SG A:CYS728 2.3 24.2 1.0 CE1 A:HIS714 3.0 24.9 1.0 CE1 A:HIS712 3.1 24.2 1.0 CD2 A:HIS712 3.1 24.8 1.0 CD2 A:HIS714 3.1 24.7 1.0 CB A:CYS728 3.1 20.7 1.0 CB A:CYS847 3.2 23.9 1.0 ND1 A:HIS714 4.2 25.0 1.0 CG A:HIS712 4.2 24.2 1.0 CG A:HIS714 4.2 23.4 1.0 ND1 A:HIS712 4.2 25.5 1.0 CD1 A:LEU839 4.3 29.1 1.0 CA A:CYS728 4.4 21.3 1.0 O A:HOH1422 4.4 42.5 1.0 O A:HOH1407 4.5 34.0 1.0 C A:CYS728 4.5 25.6 1.0 N A:ARG729 4.6 23.8 1.0 CA A:CYS847 4.6 24.3 1.0 NH2 A:ARG769 4.8 18.6 1.0 O A:HOH1448 4.9 51.4 1.0 O A:GLU843 5.0 29.7 1.0

Zinc binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Jf-31-MG46


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 Jf-31-MG46 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:39.9 occ:1.00 NE2 A:HIS441 2.1 37.1 1.0 SG A:CYS449 2.2 41.6 1.0 SG A:CYS446 2.3 39.3 1.0 OE1 A:GLU437 2.5 50.8 1.0 CE1 A:HIS441 3.0 36.8 1.0 CD A:GLU437 3.1 55.2 1.0 CD2 A:HIS441 3.1 37.5 1.0 CB A:CYS449 3.1 38.7 1.0 CG A:GLU437 3.4 42.6 1.0 CB A:CYS446 3.5 35.6 1.0 N A:CYS449 3.7 40.6 1.0 CA A:CYS446 3.8 35.9 1.0 CA A:CYS449 4.0 39.3 1.0 OE2 A:GLU437 4.1 51.8 1.0 ND1 A:HIS441 4.2 37.4 1.0 N A:GLY447 4.2 38.1 1.0 CG A:HIS441 4.2 36.0 1.0 N A:SER448 4.4 39.3 1.0 C A:CYS446 4.5 40.9 1.0 O A:HOH1200 4.5 37.2 1.0 C A:SER448 4.7 43.6 1.0 CG2 A:THR571 4.7 42.7 1.0 O A:LYS445 4.8 37.5 1.0 CB A:GLU437 4.9 36.1 1.0 CD1 A:LEU483 5.0 36.4 1.0

C.G.Noble, S.P.Lim, R.Arora, F.Yokokawa, S.Nilar, C.C.Seh, S.K.Wright, T.E.Benson, P.W.Smith, P.Y.Shi. A Conserved Pocket in the Dengue Virus Polymerase Identified Through Fragment-Based Screening. J.Biol.Chem. V. 291 8541 2016.
ISSN: ESSN 1083-351X
PubMed: 26872970
DOI: 10.1074/JBC.M115.710731