Zinc in PDB 6j00: The Rna-Dependent Rna Polymerase Domain of Dengue 3 NS5

The structure of The Rna-Dependent Rna Polymerase Domain of Dengue 3 NS5, PDB code: 6j00 was solved by H.Shimizu, S.Sekine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.52 / 2.14
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.520, 177.360, 58.010, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25

The binding sites of Zinc atom in the The Rna-Dependent Rna Polymerase Domain of Dengue 3 NS5 (pdb code 6j00). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Rna-Dependent Rna Polymerase Domain of Dengue 3 NS5, PDB code: 6j00:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Rna-Dependent Rna Polymerase Domain of Dengue 3 NS5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Rna-Dependent Rna Polymerase Domain of Dengue 3 NS5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:20.0 occ:1.00 NE2 A:HIS441 2.1 42.2 1.0 OE2 A:GLU437 2.2 46.6 1.0 SG A:CYS449 2.2 36.9 1.0 SG A:CYS446 2.4 37.7 1.0 CE1 A:HIS441 3.0 47.1 1.0 CB A:CYS449 3.1 46.0 1.0 CD A:GLU437 3.1 44.2 1.0 CD2 A:HIS441 3.2 45.1 1.0 CG A:GLU437 3.4 40.5 1.0 CB A:CYS446 3.6 41.5 1.0 N A:CYS449 3.8 42.3 1.0 CA A:CYS446 3.9 41.7 1.0 CA A:CYS449 4.0 50.4 1.0 N A:GLY447 4.1 36.8 1.0 ND1 A:HIS441 4.1 36.7 1.0 OE1 A:GLU437 4.2 48.0 1.0 CG A:HIS441 4.2 51.7 1.0 N A:SER448 4.4 43.2 1.0 C A:CYS446 4.5 41.3 1.0 C A:SER448 4.7 41.3 1.0 CD1 A:LEU483 4.9 36.5 1.0 CB A:GLU437 4.9 48.9 1.0 O A:LYS445 5.0 38.9 1.0 OG1 A:THR571 5.0 44.8 1.0

Zinc binding site 2 out of 2 in the The Rna-Dependent Rna Polymerase Domain of Dengue 3 NS5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Rna-Dependent Rna Polymerase Domain of Dengue 3 NS5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:10.7 occ:1.00 NE2 A:HIS712 2.0 35.1 1.0 NE2 A:HIS714 2.1 28.3 1.0 SG A:CYS728 2.3 23.7 1.0 SG A:CYS847 2.3 30.0 1.0 CD2 A:HIS712 2.9 33.2 1.0 CD2 A:HIS714 2.9 40.2 1.0 CE1 A:HIS712 3.0 41.2 1.0 CB A:CYS728 3.1 25.3 1.0 CE1 A:HIS714 3.2 47.5 1.0 CB A:CYS847 3.4 35.3 1.0 CG A:HIS712 4.0 36.3 1.0 ND1 A:HIS712 4.0 29.1 1.0 CG A:HIS714 4.1 33.8 1.0 ND1 A:HIS714 4.2 32.0 1.0 CD1 A:LEU839 4.2 36.0 1.0 CA A:CYS728 4.4 33.7 1.0 C A:CYS728 4.5 37.9 1.0 N A:ARG729 4.6 33.3 1.0 NH2 A:ARG769 4.7 20.4 1.0 CA A:CYS847 4.8 34.0 1.0

H.Shimizu, S.Sekine. Apo Form of DENV3 Rdrp To Be Published.