Zinc in PDB 5u04: Crystal Structure of Zika Virus NS5 Rna-Dependent Rna Polymerase

The structure of Crystal Structure of Zika Virus NS5 Rna-Dependent Rna Polymerase, PDB code: 5u04 was solved by A.S.Godoy, G.M.A.Lima, K.I.Z.Oliveira, N.U.Torres, F.V.Maluf, R.V.C.Guido, G.Oliva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.66 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.954, 78.954, 210.022, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.7

The binding sites of Zinc atom in the Crystal Structure of Zika Virus NS5 Rna-Dependent Rna Polymerase (pdb code 5u04). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Zika Virus NS5 Rna-Dependent Rna Polymerase, PDB code: 5u04:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Zika Virus NS5 Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Zika Virus NS5 Rna-Dependent Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:28.7 occ:1.00 NE2 A:HIS714 2.0 28.7 1.0 SG A:CYS730 2.4 17.4 1.0 O A:HOH1113 2.4 19.9 1.0 SG A:CYS849 2.4 18.6 1.0 CE1 A:HIS714 3.0 23.7 1.0 CD2 A:HIS714 3.0 15.6 1.0 CB A:CYS730 3.1 12.0 1.0 CB A:CYS849 3.3 21.0 1.0 OD1 A:ASN716 4.0 39.2 1.0 ND1 A:HIS714 4.1 22.2 1.0 CG A:HIS714 4.2 24.6 1.0 OE2 A:GLU845 4.2 20.8 0.4 C A:CYS730 4.2 19.1 1.0 CA A:CYS730 4.2 16.4 1.0 N A:ARG731 4.3 17.2 1.0 CD1 A:LEU841 4.4 23.0 1.0 O A:ARG731 4.6 17.6 1.0 NH1 A:ARG771 4.7 16.5 1.0 CA A:CYS849 4.7 16.9 1.0 C A:ARG731 4.7 20.6 1.0 O A:CYS730 4.7 15.6 1.0 O A:HOH1621 4.8 40.7 1.0 CA A:ARG731 4.8 12.8 1.0 O A:HOH1494 4.8 50.2 1.0 O A:GLU845 4.9 19.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Zika Virus NS5 Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Zika Virus NS5 Rna-Dependent Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:32.6 occ:1.00 OE1 A:GLU439 2.0 32.6 1.0 NE2 A:HIS443 2.0 30.8 1.0 SG A:CYS448 2.1 34.8 1.0 SG A:CYS451 2.3 29.2 1.0 CD A:GLU439 2.8 27.5 1.0 CD2 A:HIS443 2.9 25.8 1.0 CG A:GLU439 3.0 27.4 1.0 CE1 A:HIS443 3.0 26.1 1.0 CB A:CYS448 3.2 37.1 1.0 CB A:CYS451 3.3 28.8 1.0 CA A:CYS448 3.6 33.0 1.0 N A:HIS449 3.9 37.5 1.0 OE2 A:GLU439 4.0 35.4 1.0 N A:CYS451 4.0 34.3 1.0 CG A:HIS443 4.1 26.8 1.0 ND1 A:HIS443 4.1 29.2 1.0 C A:CYS448 4.2 40.4 1.0 CA A:CYS451 4.2 29.0 1.0 OH A:TYR453 4.3 39.8 1.0 O A:HOH1502 4.4 39.3 1.0 CD1 A:LEU485 4.5 28.4 1.0 CB A:GLU439 4.5 32.3 1.0 O A:GLU447 4.8 33.7 1.0 N A:SER450 4.8 36.4 1.0 O A:GLU439 4.8 27.3 1.0 N A:CYS448 4.9 31.3 1.0

A.S.Godoy, G.M.Lima, K.I.Oliveira, N.U.Torres, F.V.Maluf, R.V.Guido, G.Oliva. Crystal Structure of Zika Virus NS5 Rna-Dependent Rna Polymerase. Nat Commun V. 8 14764 2017.
ISSN: ESSN 2041-1723
PubMed: 28345596
DOI: 10.1038/NCOMMS14764