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Zinc in PDB 6izy: The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5

Protein crystallography data

The structure of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, PDB code: 6izy was solved by H.Shimizu, S.Sekine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.96 / 2.11
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 237.350, 237.350, 237.350, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.1

Other elements in 6izy:

The structure of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5 also contains other interesting chemical elements:

Cobalt (Co) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5 (pdb code 6izy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, PDB code: 6izy:

Zinc binding site 1 out of 1 in 6izy

Go back to Zinc Binding Sites List in 6izy
Zinc binding site 1 out of 1 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn905

b:53.4
occ:1.00
NE2 A:HIS442 2.1 63.0 1.0
SG A:CYS447 2.2 47.7 1.0
SG A:CYS450 2.3 50.4 1.0
OE1 A:GLU438 2.6 55.9 1.0
CE1 A:HIS442 3.1 56.3 1.0
CD2 A:HIS442 3.1 59.6 1.0
CB A:CYS450 3.1 54.5 1.0
CB A:CYS447 3.2 57.2 1.0
CD A:GLU438 3.3 64.0 1.0
CG A:GLU438 3.5 59.9 1.0
CA A:CYS447 3.7 60.0 1.0
N A:CYS450 3.7 48.5 1.0
N A:GLU448 3.9 54.7 1.0
CA A:CYS450 4.0 56.6 1.0
ND1 A:HIS442 4.2 56.5 1.0
CG A:HIS442 4.2 64.4 1.0
C A:CYS447 4.3 56.9 1.0
N A:THR449 4.4 51.7 1.0
OE2 A:GLU438 4.4 69.5 1.0
CG2 A:THR572 4.5 59.0 1.0
C A:THR449 4.8 52.9 1.0
O A:LYS446 4.9 57.2 1.0
OG1 A:THR449 4.9 63.0 1.0
N A:CYS447 5.0 57.9 1.0

Reference:

H.Shimizu, S.Sekine. Apo Form of DENV2 Rdrp To Be Published.
Page generated: Wed Dec 16 12:02:28 2020

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