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Zinc in PDB 5dto: Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah

Protein crystallography data

The structure of Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah, PDB code: 5dto was solved by Y.Zhao, T.S.Soh, S.P.Lim, K.Y.Chung, K.Swaminathan, S.G.Vasudevan, P.-Y.Shi, J.Lescar, D.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.33 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.660, 151.394, 69.432, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 24.4

Other elements in 5dto:

The structure of Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah (pdb code 5dto). 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 Full Length NS5 Complexed with Viral Cap 0-Rna and Sah, PDB code: 5dto:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5dto

Go back to Zinc Binding Sites List in 5dto
Zinc binding site 1 out of 2 in the Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:31.5
occ:1.00
OE2 A:GLU437 2.0 35.2 1.0
NE2 A:HIS441 2.1 28.0 1.0
SG A:CYS449 2.2 25.1 1.0
SG A:CYS446 2.4 31.0 1.0
CE1 A:HIS441 2.9 24.6 1.0
CD A:GLU437 3.1 36.9 1.0
CD2 A:HIS441 3.2 25.7 1.0
CB A:CYS449 3.2 35.7 1.0
CB A:CYS446 3.5 25.6 1.0
CG A:GLU437 3.6 36.2 1.0
CA A:CYS446 3.8 26.6 1.0
N A:CYS449 4.0 42.9 1.0
N A:GLY447 4.0 28.7 1.0
ND1 A:HIS441 4.1 24.8 1.0
OE1 A:GLU437 4.2 38.5 1.0
CA A:CYS449 4.2 42.2 1.0
CG A:HIS441 4.2 26.1 1.0
C A:CYS446 4.3 29.2 1.0
N A:SER448 4.3 29.9 1.0
CG2 A:THR571 4.4 38.3 1.0
C A:SER448 4.6 37.9 1.0
O A:HOH1250 4.7 25.5 1.0
O A:LYS445 4.9 36.0 1.0
O A:GLU437 5.0 27.8 1.0

Zinc binding site 2 out of 2 in 5dto

Go back to Zinc Binding Sites List in 5dto
Zinc binding site 2 out of 2 in the Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:42.7
occ:1.00
NE2 A:HIS714 2.0 44.6 1.0
NE2 A:HIS712 2.0 45.2 1.0
SG A:CYS847 2.3 54.8 1.0
SG A:CYS728 2.4 41.1 1.0
CD2 A:HIS712 2.9 39.2 1.0
CE1 A:HIS714 2.9 44.6 1.0
CD2 A:HIS714 3.0 41.4 1.0
CE1 A:HIS712 3.1 44.9 1.0
CB A:CYS728 3.1 35.1 1.0
CB A:CYS847 3.5 50.2 1.0
CG A:HIS712 4.0 37.2 1.0
ND1 A:HIS714 4.1 38.9 1.0
ND1 A:HIS712 4.1 41.8 1.0
CG A:HIS714 4.1 37.3 1.0
O A:HOH1312 4.1 38.0 1.0
CD1 A:LEU839 4.3 41.2 1.0
N A:ARG729 4.3 40.4 1.0
CA A:CYS728 4.3 33.1 1.0
C A:CYS728 4.3 34.2 1.0
NH1 A:ARG769 4.7 35.7 1.0
CA A:CYS847 4.8 50.2 1.0
O A:ARG729 4.8 40.5 1.0
O A:CYS728 4.9 34.2 1.0
CA A:ARG729 5.0 43.9 1.0

Reference:

Y.Zhao, T.S.Soh, S.P.Lim, K.Y.Chung, K.Swaminathan, S.G.Vasudevan, P.-Y.Shi, J.Lescar, D.Luo. Molecular Basis For Specific Viral Rna Recognition and 2'-O-Ribose Methylation By the Dengue Virus Nonstructural Protein 5 (NS5) Proc.Natl.Acad.Sci.Usa V. 112 14834 2015.
ISSN: ESSN 1091-6490
PubMed: 26578813
DOI: 10.1073/PNAS.1514978112
Page generated: Wed Dec 16 06:08:48 2020

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