Zinc in PDB 6ld4: Zika NS5 Polymerase Domain

All present enzymatic activity of Zika NS5 Polymerase Domain:
2.1.1.56; 2.1.1.57; 2.7.7.48;

The structure of Zika NS5 Polymerase Domain, PDB code: 6ld4 was solved by A.El Sahili, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.91 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.100, 85.170, 69.810, 90.00, 113.34, 90.00
R / Rfree (%)	19.6 / 22.4

The binding sites of Zinc atom in the Zika NS5 Polymerase Domain (pdb code 6ld4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Zika NS5 Polymerase Domain, PDB code: 6ld4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Zika NS5 Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zika NS5 Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:34.2 occ:1.00 NE2 A:HIS443 2.1 36.7 1.0 OE1 A:GLU439 2.2 33.3 1.0 SG A:CYS448 2.2 36.1 1.0 SG A:CYS451 2.4 34.7 1.0 CE1 A:HIS443 3.0 36.0 1.0 CD2 A:HIS443 3.1 36.9 1.0 CD A:GLU439 3.2 54.6 1.0 CB A:CYS451 3.2 31.9 1.0 CB A:CYS448 3.3 33.5 1.0 CG A:GLU439 3.5 39.8 1.0 N A:CYS451 3.7 35.5 1.0 CA A:CYS448 3.7 34.3 1.0 O A:HOH1052 3.9 45.1 1.0 CA A:CYS451 4.1 32.8 1.0 N A:GLN449 4.2 33.5 1.0 ND1 A:HIS443 4.2 36.7 1.0 CG A:HIS443 4.2 35.7 1.0 O A:HOH1253 4.3 39.5 1.0 OE2 A:GLU439 4.3 46.8 1.0 C A:CYS448 4.3 36.1 1.0 N A:SER450 4.3 37.6 1.0 CD2 A:TYR572 4.6 39.2 1.0 C A:SER450 4.7 39.8 1.0 CB A:TYR572 4.7 35.6 1.0 CG A:TYR572 4.9 38.0 1.0 O A:GLU447 5.0 36.6 1.0

Zinc binding site 2 out of 2 in the Zika NS5 Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zika NS5 Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:24.8 occ:0.98 O A:HOH1027 2.1 28.1 1.0 NE2 A:HIS714 2.1 26.8 1.0 SG A:CYS730 2.3 23.5 1.0 SG A:CYS849 2.3 26.1 1.0 CE1 A:HIS714 3.0 26.0 1.0 CD2 A:HIS714 3.2 27.2 1.0 CB A:CYS730 3.2 20.3 1.0 CB A:CYS849 3.3 23.6 1.0 O A:HOH1526 3.8 31.0 1.0 ND1 A:HIS714 4.2 26.6 1.0 CG A:HIS714 4.3 25.4 1.0 C A:CYS730 4.3 23.6 1.0 CA A:CYS730 4.4 18.9 1.0 OD1 A:ASN716 4.4 31.6 1.0 CD1 A:LEU841 4.4 24.7 1.0 N A:ARG731 4.4 22.3 1.0 O A:HOH1575 4.5 36.0 1.0 O A:HOH1607 4.6 32.9 1.0 NH2 A:ARG771 4.7 21.9 1.0 O A:ARG731 4.7 22.5 1.0 CA A:CYS849 4.7 23.2 1.0 O A:CYS730 4.8 23.4 1.0 O A:GLU845 4.8 25.6 1.0 C A:ARG731 4.9 24.2 1.0 CA A:ARG731 4.9 22.4 1.0

A.Gharbi-Ayachi, S.Santhanakrishnan, Y.H.Wong, K.W.K.Chan, S.T.Tan, R.W.Bates, S.G.Vasudevan, A.El Sahili, J.Lescar. Non-Nucleoside Inhibitors of Zika Virus Rna-Dependent Rna Polymerase. J.Virol. V. 94 2020.
ISSN: ESSN 1098-5514
PubMed: 32796069
DOI: 10.1128/JVI.00794-20