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Zinc in PDB 2j7w: Dengue Virus NS5 Rna Dependent Rna Polymerase Domain Complexed with 3'Dgtp

Protein crystallography data

The structure of Dengue Virus NS5 Rna Dependent Rna Polymerase Domain Complexed with 3'Dgtp, PDB code: 2j7w 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 / 2.6
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 163.716, 180.918, 58.042, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 28.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Dengue Virus NS5 Rna Dependent Rna Polymerase Domain Complexed with 3'Dgtp (pdb code 2j7w). 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 Complexed with 3'Dgtp, PDB code: 2j7w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2j7w

Go back to Zinc Binding Sites List in 2j7w
Zinc binding site 1 out of 2 in the Dengue Virus NS5 Rna Dependent Rna Polymerase Domain Complexed with 3'Dgtp


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 Complexed with 3'Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1884

b:45.5
occ:1.00
NE2 A:HIS712 1.9 60.1 1.0
NE2 A:HIS714 2.0 57.0 1.0
SG A:CYS847 2.1 58.2 1.0
SG A:CYS728 2.3 54.2 1.0
CD2 A:HIS712 2.9 59.0 1.0
CE1 A:HIS714 3.0 57.4 1.0
CE1 A:HIS712 3.0 59.6 1.0
CD2 A:HIS714 3.1 57.3 1.0
CB A:CYS728 3.2 55.1 1.0
CB A:CYS847 3.4 58.5 1.0
CG A:HIS712 4.0 58.4 1.0
ND1 A:HIS712 4.1 57.2 1.0
ND1 A:HIS714 4.1 56.9 1.0
CG A:HIS714 4.2 58.3 1.0
CD1 A:LEU839 4.2 59.8 1.0
CA A:CYS728 4.5 54.9 1.0
C A:CYS728 4.5 55.4 1.0
N A:ARG729 4.7 55.0 1.0
CA A:CYS847 4.7 58.3 1.0
NH2 A:ARG769 4.8 53.9 1.0
O A:CYS728 4.9 55.5 1.0

Zinc binding site 2 out of 2 in 2j7w

Go back to Zinc Binding Sites List in 2j7w
Zinc binding site 2 out of 2 in the Dengue Virus NS5 Rna Dependent Rna Polymerase Domain Complexed with 3'Dgtp


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 Complexed with 3'Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1885

b:63.1
occ:0.60
NE2 A:HIS441 2.0 60.9 1.0
SG A:CYS449 2.1 65.5 1.0
OE1 A:GLU437 2.3 61.7 1.0
SG A:CYS446 2.4 60.0 1.0
CD2 A:HIS441 2.9 60.7 1.0
CE1 A:HIS441 3.0 59.9 1.0
CB A:CYS449 3.2 64.6 1.0
CD A:GLU437 3.3 61.3 1.0
CG A:GLU437 3.5 60.9 1.0
CB A:CYS446 3.5 61.1 1.0
CA A:CYS446 3.8 61.0 1.0
N A:GLY447 3.9 61.7 1.0
N A:CYS449 3.9 64.2 1.0
CG A:HIS441 4.1 60.4 1.0
ND1 A:HIS441 4.1 59.2 1.0
CA A:CYS449 4.2 64.6 1.0
C A:CYS446 4.3 61.4 1.0
OE2 A:GLU437 4.4 60.9 1.0
N A:SER448 4.5 63.1 1.0
CG2 A:THR571 4.9 60.3 1.0
O A:LYS445 4.9 61.0 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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