Zinc in PDB 5f41: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Fd-83-KI26

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Fd-83-KI26, PDB code: 5f41 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)	40.00 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.700, 178.330, 57.930, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.4

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Fd-83-KI26 (pdb code 5f41). 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 Fd-83-KI26, PDB code: 5f41:
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 Fd-83-KI26


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 Fd-83-KI26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:23.9 occ:1.00 NE2 A:HIS712 2.0 22.3 1.0 NE2 A:HIS714 2.1 24.2 1.0 SG A:CYS847 2.3 25.3 1.0 SG A:CYS728 2.3 24.5 1.0 CE1 A:HIS714 3.0 24.7 1.0 CE1 A:HIS712 3.0 22.2 1.0 CD2 A:HIS712 3.1 22.4 1.0 CB A:CYS728 3.1 21.8 1.0 CD2 A:HIS714 3.1 23.7 1.0 CB A:CYS847 3.3 21.4 1.0 ND1 A:HIS712 4.2 22.8 1.0 ND1 A:HIS714 4.2 25.3 1.0 CG A:HIS712 4.2 21.9 1.0 CG A:HIS714 4.2 23.1 1.0 CD1 A:LEU839 4.3 26.1 1.0 CA A:CYS728 4.4 22.5 1.0 O A:HOH1384 4.5 31.0 1.0 C A:CYS728 4.5 26.0 1.0 N A:ARG729 4.6 21.6 1.0 CA A:CYS847 4.7 21.4 1.0 NH2 A:ARG769 4.8 18.4 1.0 O A:HOH1445 4.8 48.9 1.0 O A:HOH1164 4.9 46.5 1.0 O A:ARG729 5.0 24.4 1.0 O A:GLU843 5.0 27.6 1.0

Zinc binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Fd-83-KI26


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 Fd-83-KI26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:37.5 occ:1.00 NE2 A:HIS441 2.1 38.3 1.0 OE1 A:GLU437 2.2 54.9 1.0 SG A:CYS449 2.2 41.3 1.0 SG A:CYS446 2.3 38.4 1.0 CD A:GLU437 3.0 46.8 1.0 CE1 A:HIS441 3.1 38.2 1.0 CB A:CYS449 3.1 37.9 1.0 CD2 A:HIS441 3.2 38.2 1.0 CG A:GLU437 3.3 36.5 1.0 CB A:CYS446 3.5 34.9 1.0 N A:CYS449 3.7 39.0 1.0 CA A:CYS446 3.8 35.0 1.0 CA A:CYS449 4.0 38.2 1.0 N A:GLY447 4.1 38.5 1.0 OE2 A:GLU437 4.2 49.8 1.0 ND1 A:HIS441 4.2 38.6 1.0 CG A:HIS441 4.3 36.6 1.0 N A:SER448 4.5 40.5 1.0 C A:CYS446 4.5 41.2 1.0 O A:HOH1256 4.6 36.2 1.0 C A:SER448 4.7 43.9 1.0 CG2 A:THR571 4.8 42.4 1.0 CB A:GLU437 4.9 33.9 1.0 O A:LYS445 5.0 40.6 1.0 CD1 A:LEU483 5.0 32.0 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