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Zinc in PDB 2j7u: Dengue Virus NS5 Rna Dependent Rna Polymerase Domain

Protein crystallography data

The structure of Dengue Virus NS5 Rna Dependent Rna Polymerase Domain, PDB code: 2j7u was solved by T.L.Yap, T.Xu, Y.L.Chen, H.Malet, M.P.Egloff, B.Canard, S.G.Vasudevan, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 160.150, 180.478, 57.987, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.4

Other elements in 2j7u:

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

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Dengue Virus NS5 Rna Dependent Rna Polymerase Domain (pdb code 2j7u). 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 Virus NS5 Rna Dependent Rna Polymerase Domain, PDB code: 2j7u:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2j7u

Go back to Zinc Binding Sites List in 2j7u
Zinc binding site 1 out of 2 in the Dengue Virus NS5 Rna Dependent Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dengue Virus NS5 Rna Dependent Rna Polymerase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1884

b:25.1
occ:1.00
NE2 A:HIS712 2.0 35.4 1.0
NE2 A:HIS714 2.1 33.6 1.0
SG A:CYS847 2.3 35.1 1.0
SG A:CYS728 2.4 33.3 1.0
CD2 A:HIS712 3.0 35.1 1.0
CD2 A:HIS714 3.0 33.3 1.0
CE1 A:HIS712 3.1 36.2 1.0
CB A:CYS728 3.2 33.4 1.0
CE1 A:HIS714 3.2 35.5 1.0
CB A:CYS847 3.3 33.4 1.0
CG A:HIS712 4.1 35.0 1.0
ND1 A:HIS712 4.1 34.9 1.0
CG A:HIS714 4.2 33.4 1.0
ND1 A:HIS714 4.2 34.0 1.0
CD1 A:LEU839 4.3 35.9 1.0
O A:HOH2384 4.4 40.0 1.0
O A:HOH2482 4.4 34.0 1.0
O A:HOH2360 4.5 44.0 1.0
CA A:CYS728 4.5 33.7 1.0
C A:CYS728 4.6 34.0 1.0
N A:ARG729 4.6 34.7 1.0
CA A:CYS847 4.7 33.3 1.0
NH2 A:ARG769 4.7 32.4 1.0

Zinc binding site 2 out of 2 in 2j7u

Go back to Zinc Binding Sites List in 2j7u
Zinc binding site 2 out of 2 in the Dengue Virus NS5 Rna Dependent Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dengue Virus NS5 Rna Dependent Rna Polymerase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1885

b:31.8
occ:0.60
NE2 A:HIS441 2.0 36.0 1.0
SG A:CYS449 2.2 38.8 1.0
OE1 A:GLU437 2.3 36.7 1.0
SG A:CYS446 2.4 37.2 1.0
CD2 A:HIS441 2.9 36.3 1.0
CE1 A:HIS441 3.0 36.0 1.0
CB A:CYS449 3.2 38.9 1.0
CD A:GLU437 3.2 36.3 1.0
CG A:GLU437 3.5 35.5 1.0
CB A:CYS446 3.6 37.4 1.0
N A:CYS449 3.9 38.9 1.0
CA A:CYS446 3.9 37.4 1.0
N A:GLY447 3.9 37.8 1.0
ND1 A:HIS441 4.1 36.1 1.0
CG A:HIS441 4.1 36.6 1.0
CA A:CYS449 4.1 38.9 1.0
OE2 A:GLU437 4.3 36.3 1.0
N A:SER448 4.4 38.4 1.0
C A:CYS446 4.4 37.6 1.0
CG2 A:THR571 4.7 38.7 1.0
C A:SER448 4.8 38.8 1.0
O A:HOH2097 4.8 48.5 1.0
O A:HOH2098 4.9 35.6 1.0
O A:GLU437 4.9 34.7 1.0
O A:LYS445 5.0 37.0 1.0

Reference:

T.L.Yap, T.Xu, Y.L.Chen, H.Malet, M.P.Egloff, B.Canard, S.G.Vasudevan, J.Lescar. Crystal Structure of the Dengue Virus Rna- Dependent Rna Polymerase Catalytic Domain at 1.85 Angstrom Resolution. J.Virol. V. 81 4753 2007.
ISSN: ISSN 0022-538X
PubMed: 17301146
DOI: 10.1128/JVI.02283-06
Page generated: Wed Dec 16 03:31:41 2020

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