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Zinc in PDB 4hhj: Dengue Serotype 3 Rna-Dependent Rna Polymerase

Enzymatic activity of Dengue Serotype 3 Rna-Dependent Rna Polymerase

All present enzymatic activity of Dengue Serotype 3 Rna-Dependent Rna Polymerase:
2.7.7.48;

Protein crystallography data

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

Resolution Low / High (Å) 29.85 / 1.79
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 161.320, 177.610, 57.820, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase (pdb code 4hhj). 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, PDB code: 4hhj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4hhj

Go back to Zinc Binding Sites List in 4hhj
Zinc binding site 1 out of 2 in the Dengue Serotype 3 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 Dengue Serotype 3 Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:22.4
occ:1.00
NE2 A:HIS714 2.0 24.3 1.0
NE2 A:HIS712 2.1 22.8 1.0
SG A:CYS847 2.3 24.6 1.0
SG A:CYS728 2.3 21.4 1.0
CE1 A:HIS714 3.0 24.4 1.0
CD2 A:HIS712 3.0 22.9 1.0
CD2 A:HIS714 3.1 23.9 1.0
CE1 A:HIS712 3.1 22.8 1.0
CB A:CYS728 3.1 17.4 1.0
CB A:CYS847 3.3 21.5 1.0
CG A:HIS712 4.2 21.3 1.0
ND1 A:HIS714 4.2 25.6 1.0
CG A:HIS714 4.2 23.3 1.0
ND1 A:HIS712 4.2 23.1 1.0
CD1 A:LEU839 4.3 24.6 1.0
O A:HOH1514 4.4 28.9 1.0
CA A:CYS728 4.4 17.1 1.0
O A:HOH1194 4.4 28.9 1.0
C A:CYS728 4.6 20.5 1.0
N A:ARG729 4.6 18.7 1.0
CA A:CYS847 4.7 21.5 1.0
NH2 A:ARG769 4.7 18.6 1.0
O A:HOH1256 4.8 32.9 1.0
O13 A:P6G1003 4.9 30.0 0.5

Zinc binding site 2 out of 2 in 4hhj

Go back to Zinc Binding Sites List in 4hhj
Zinc binding site 2 out of 2 in the Dengue Serotype 3 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 Dengue Serotype 3 Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:33.5
occ:1.00
NE2 A:HIS441 2.1 31.2 1.0
SG A:CYS449 2.2 35.0 1.0
OE1 A:GLU437 2.2 38.9 1.0
SG A:CYS446 2.3 35.1 1.0
CE1 A:HIS441 3.0 31.3 1.0
CD2 A:HIS441 3.1 31.3 1.0
CB A:CYS449 3.1 32.2 1.0
CD A:GLU437 3.1 46.2 1.0
CG A:GLU437 3.4 33.9 1.0
CB A:CYS446 3.5 31.1 1.0
N A:CYS449 3.7 35.7 1.0
CA A:CYS446 3.8 32.4 1.0
CA A:CYS449 4.0 33.1 1.0
N A:GLY447 4.1 38.5 1.0
ND1 A:HIS441 4.2 31.7 1.0
CG A:HIS441 4.2 30.7 1.0
OE2 A:GLU437 4.3 33.6 1.0
N A:SER448 4.4 40.0 1.0
C A:CYS446 4.4 39.7 1.0
O A:HOH1471 4.6 41.1 1.0
O A:HOH1207 4.6 33.1 1.0
C A:SER448 4.7 41.0 1.0
CG2 A:THR571 4.8 36.7 1.0
O A:LYS445 4.9 35.8 1.0
CB A:GLU437 5.0 30.5 1.0

Reference:

C.G.Noble, S.P.Lim, Y.L.Chen, C.W.Liew, L.Yap, J.Lescar, P.-Y.Shi. Conformational Flexibility of the Dengue Virus Rna-Dependent Rna Polymerase Revealed By A Complex with An Inhibitor J.Virol. V. 87 5291 2013.
ISSN: ISSN 0022-538X
PubMed: 23408636
DOI: 10.1128/JVI.00045-13
Page generated: Wed Dec 16 05:22:13 2020

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