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Zinc in PDB 6ld2: Zika NS5 Polymerase Domain

Enzymatic activity of 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;

Protein crystallography data

The structure of Zika NS5 Polymerase Domain, PDB code: 6ld2 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) 55.65 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.940, 85.060, 69.740, 90.00, 113.44, 90.00
R / Rfree (%) 20.2 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Zika NS5 Polymerase Domain (pdb code 6ld2). 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: 6ld2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6ld2

Go back to Zinc Binding Sites List in 6ld2
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:31.0
occ:1.00
OE1 A:GLU439 2.0 34.0 1.0
NE2 A:HIS443 2.1 33.2 1.0
SG A:CYS448 2.3 31.1 1.0
SG A:CYS451 2.3 31.1 1.0
CE1 A:HIS443 3.1 33.0 1.0
CD A:GLU439 3.1 38.9 1.0
CD2 A:HIS443 3.1 32.6 1.0
CB A:CYS451 3.2 31.6 1.0
CB A:CYS448 3.4 33.2 1.0
CG A:GLU439 3.5 35.8 1.0
N A:CYS451 3.7 32.9 1.0
CA A:CYS448 3.8 33.8 1.0
O A:HOH1090 4.0 41.1 1.0
CA A:CYS451 4.0 31.3 1.0
OE2 A:GLU439 4.2 42.1 1.0
N A:GLN449 4.2 33.3 1.0
ND1 A:HIS443 4.2 32.8 1.0
CG A:HIS443 4.2 31.6 1.0
O A:HOH1232 4.3 42.0 1.0
N A:SER450 4.4 34.4 1.0
C A:CYS448 4.4 33.2 1.0
CD2 A:TYR572 4.5 37.8 1.0
C A:SER450 4.6 33.8 1.0
CB A:TYR572 4.7 33.6 1.0
CG A:TYR572 4.8 36.0 1.0
O A:GLU447 5.0 36.6 1.0
CB A:GLU439 5.0 35.9 1.0

Zinc binding site 2 out of 2 in 6ld2

Go back to Zinc Binding Sites List in 6ld2
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:21.3
occ:1.00
NE2 A:HIS714 2.1 20.4 1.0
SG A:CYS730 2.3 20.6 1.0
SG A:CYS849 2.3 21.3 1.0
CE1 A:HIS714 3.0 21.9 1.0
CD2 A:HIS714 3.2 21.6 1.0
CB A:CYS730 3.2 19.9 1.0
CB A:CYS849 3.4 22.1 1.0
O A:HOH1496 3.8 30.9 1.0
ND1 A:HIS714 4.2 20.9 1.0
CG A:HIS714 4.2 19.8 1.0
C A:CYS730 4.3 19.8 1.0
CA A:CYS730 4.3 18.3 1.0
N A:ARG731 4.4 19.7 1.0
OD1 A:ASN716 4.4 25.4 1.0
CD1 A:LEU841 4.4 21.7 1.0
O A:HOH1542 4.5 37.8 1.0
O A:HOH1568 4.7 33.3 1.0
O A:CYS730 4.7 20.1 1.0
O A:ARG731 4.7 20.2 1.0
CA A:CYS849 4.7 21.6 1.0
C A:ARG731 4.8 19.5 1.0
CA A:ARG731 4.8 20.1 1.0
O A:GLU845 4.8 22.1 1.0
NH2 A:ARG771 4.8 20.3 1.0

Reference:

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
Page generated: Wed Dec 16 12:14:23 2020

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