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Zinc in PDB 5hn0: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 4

Enzymatic activity of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 4

All present enzymatic activity of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 4:
2.7.7.48;

Protein crystallography data

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 4, PDB code: 5hn0 was solved by C.G.Noble, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.66 / 2.05
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 161.400, 177.850, 57.730, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 4 (pdb code 5hn0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 4, PDB code: 5hn0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5hn0

Go back to Zinc Binding Sites List in 5hn0
Zinc binding site 1 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:27.6
occ:1.00
NE2 A:HIS712 2.0 25.4 1.0
NE2 A:HIS714 2.0 25.3 1.0
SG A:CYS728 2.3 26.4 1.0
SG A:CYS847 2.3 29.3 1.0
CE1 A:HIS712 3.0 24.7 1.0
CE1 A:HIS714 3.0 25.5 1.0
CD2 A:HIS714 3.1 25.3 1.0
CD2 A:HIS712 3.1 25.6 1.0
CB A:CYS728 3.1 23.0 1.0
CB A:CYS847 3.2 25.3 1.0
ND1 A:HIS712 4.1 26.0 1.0
CG A:HIS712 4.2 25.1 1.0
ND1 A:HIS714 4.2 26.0 1.0
CG A:HIS714 4.2 24.6 1.0
CD1 A:LEU839 4.2 30.1 1.0
O A:HOH1403 4.4 33.5 1.0
CA A:CYS728 4.4 22.9 1.0
C A:CYS728 4.6 28.8 1.0
CA A:CYS847 4.6 25.0 1.0
N A:ARG729 4.6 26.1 1.0
NH2 A:ARG769 4.7 22.6 1.0
O A:HOH1475 4.9 53.0 1.0
O A:GLU843 4.9 29.0 1.0
O A:ARG729 4.9 31.0 1.0

Zinc binding site 2 out of 2 in 5hn0

Go back to Zinc Binding Sites List in 5hn0
Zinc binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:41.1
occ:1.00
NE2 A:HIS441 2.1 38.1 1.0
SG A:CYS449 2.2 42.5 1.0
SG A:CYS446 2.3 39.1 1.0
OE1 A:GLU437 2.5 53.4 1.0
CB A:CYS449 3.1 39.7 1.0
CE1 A:HIS441 3.1 37.5 1.0
CD A:GLU437 3.2 53.5 1.0
CD2 A:HIS441 3.2 38.2 1.0
CG A:GLU437 3.4 45.0 1.0
CB A:CYS446 3.5 35.6 1.0
N A:CYS449 3.7 41.1 1.0
CA A:CYS446 3.8 36.1 1.0
CA A:CYS449 4.0 40.3 1.0
N A:GLY447 4.1 39.6 1.0
OE2 A:GLU437 4.2 51.7 1.0
ND1 A:HIS441 4.3 37.8 1.0
CG A:HIS441 4.3 36.7 1.0
N A:SER448 4.4 43.2 1.0
C A:CYS446 4.4 41.8 1.0
O A:HOH1135 4.7 40.4 1.0
C A:SER448 4.7 44.8 1.0
CG2 A:THR571 4.8 45.9 1.0
CB A:GLU437 4.9 36.0 1.0
O A:LYS445 4.9 38.1 1.0

Reference:

F.Yokokawa, S.Nilar, C.G.Noble, S.P.Lim, R.Rao, S.Tania, G.Wang, G.Lee, J.Hunziker, R.Karuna, U.Manjunatha, P.Y.Shi, P.W.Smith. Discovery of Potent Non-Nucleoside Inhibitors of Dengue Viral Rna-Dependent Rna Polymerase From A Fragment Hit Using Structure-Based Drug Design. J.Med.Chem. V. 59 3935 2016.
ISSN: ISSN 0022-2623
PubMed: 26984786
DOI: 10.1021/ACS.JMEDCHEM.6B00143
Page generated: Wed Dec 16 06:20:34 2020

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