Zinc in PDB 6ld3: 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: 6ld3 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)	51.18 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.650, 84.990, 69.780, 90.00, 113.28, 90.00
R / Rfree (%)	19.2 / 24.9

The binding sites of Zinc atom in the Zika NS5 Polymerase Domain (pdb code 6ld3). 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: 6ld3:
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:50.9 occ:1.00 NE2 A:HIS443 1.9 49.0 1.0 OE1 A:GLU439 2.1 57.3 1.0 SG A:CYS448 2.3 47.8 1.0 SG A:CYS451 2.3 48.2 1.0 CE1 A:HIS443 2.8 49.3 1.0 CD2 A:HIS443 3.0 48.0 1.0 CD A:GLU439 3.1 57.5 1.0 CB A:CYS451 3.1 48.0 1.0 CG A:GLU439 3.4 52.6 1.0 CB A:CYS448 3.5 51.3 1.0 N A:CYS451 3.6 49.3 1.0 CA A:CYS448 3.9 52.4 1.0 CA A:CYS451 3.9 48.7 1.0 ND1 A:HIS443 4.0 49.4 1.0 CG A:HIS443 4.1 47.6 1.0 OE2 A:GLU439 4.2 60.6 1.0 N A:GLN449 4.2 52.1 1.0 N A:SER450 4.4 51.1 1.0 C A:CYS448 4.5 52.2 1.0 C A:SER450 4.6 50.3 1.0 CD2 A:TYR572 4.8 55.3 1.0 CB A:TYR572 4.9 52.7 1.0 O A:HOH1128 4.9 47.2 1.0 CB A:GLU439 4.9 51.0 1.0 O A:GLU447 5.0 54.6 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:41.1 occ:1.00 O A:HOH1053 2.0 37.1 1.0 NE2 A:HIS714 2.0 36.7 1.0 SG A:CYS849 2.2 43.6 1.0 SG A:CYS730 2.3 38.1 1.0 CE1 A:HIS714 2.8 35.9 1.0 CD2 A:HIS714 3.1 35.5 1.0 CB A:CYS730 3.2 34.8 1.0 CB A:CYS849 3.3 37.5 1.0 O A:HOH1184 4.0 55.5 1.0 ND1 A:HIS714 4.0 34.9 1.0 OD1 A:ASN716 4.0 48.6 1.0 CG A:HIS714 4.1 33.8 1.0 C A:CYS730 4.3 34.4 1.0 CA A:CYS730 4.3 34.0 1.0 N A:ARG731 4.4 33.6 1.0 CD1 A:LEU841 4.4 33.7 1.0 O A:ARG731 4.7 34.5 1.0 CA A:CYS849 4.7 36.7 1.0 O A:HOH1199 4.7 43.2 1.0 NH2 A:ARG771 4.8 30.3 1.0 O A:CYS730 4.8 34.6 1.0 O A:GLU845 4.9 36.1 1.0 C A:ARG731 4.9 34.7 1.0 CA A:ARG731 4.9 34.7 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