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Zinc in PDB 5f9f: Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna

Enzymatic activity of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna

All present enzymatic activity of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna, PDB code: 5f9f was solved by C.Wang, J.Marcotrigiano, M.T.Miller, F.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.99 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.524, 174.252, 308.288, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25.9

Other elements in 5f9f:

The structure of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Magnesium (Mg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna (pdb code 5f9f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna, PDB code: 5f9f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5f9f

Go back to Zinc Binding Sites List in 5f9f
Zinc binding site 1 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:97.2
occ:1.00
 SG A:CYS813 2.3 73.2 1.0
SG A:CYS810 2.3 85.7 1.0
SG A:CYS864 2.3 55.2 1.0
SG A:CYS869 2.4 57.5 1.0
CB A:CYS864 2.9 53.0 1.0
CB A:CYS869 3.1 71.1 1.0
CB A:CYS810 3.1 28.5 1.0
CB A:CYS813 3.6 22.1 1.0
N A:CYS813 4.0 51.4 1.0
CB A:HIS871 4.2 34.0 1.0
CA A:CYS864 4.4 52.9 1.0
CA A:CYS813 4.4 48.4 1.0
CB A:LYS812 4.5 40.5 1.0
NE1 A:TRP873 4.6 42.0 1.0
CA A:CYS869 4.6 68.8 1.0
CA A:CYS810 4.6 43.2 1.0
CZ2 A:TRP873 4.7 39.1 1.0
CB A:ALA815 4.9 35.8 1.0
C A:LYS812 4.9 51.3 1.0
N A:HIS871 5.0 37.1 1.0
CE2 A:TRP873 5.0 37.2 1.0

Zinc binding site 2 out of 6 in 5f9f

Go back to Zinc Binding Sites List in 5f9f
Zinc binding site 2 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:99.4
occ:1.00
 SG C:CYS813 2.3 61.8 1.0
SG C:CYS869 2.3 47.3 1.0
SG C:CYS810 2.3 57.2 1.0
SG C:CYS864 2.4 78.8 1.0
CB C:CYS864 2.9 51.3 1.0
CB C:CYS810 3.1 43.8 1.0
CB C:CYS869 3.1 60.7 1.0
CB C:CYS813 3.6 56.2 1.0
N C:CYS813 3.9 57.1 1.0
CA C:CYS813 4.3 56.8 1.0
CB C:HIS871 4.4 33.6 1.0
CA C:CYS864 4.4 48.8 1.0
CZ2 C:TRP873 4.5 44.9 1.0
NE1 C:TRP873 4.5 42.0 1.0
CA C:CYS810 4.5 48.6 1.0
CA C:CYS869 4.6 60.6 1.0
CB C:LYS812 4.6 37.4 1.0
CB C:ALA815 4.8 21.2 1.0
CE2 C:TRP873 4.8 46.7 1.0
C C:CYS813 4.9 57.4 1.0
C C:LYS812 4.9 58.5 1.0
N C:HIS871 5.0 45.5 1.0
C C:CYS869 5.0 47.5 1.0

Zinc binding site 3 out of 6 in 5f9f

Go back to Zinc Binding Sites List in 5f9f
Zinc binding site 3 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:95.7
occ:1.00
 SG E:CYS864 2.3 82.4 1.0
SG E:CYS813 2.4 59.2 1.0
SG E:CYS869 2.4 75.9 1.0
SG E:CYS810 2.4 87.2 1.0
CB E:CYS864 2.9 77.5 1.0
CB E:CYS869 3.0 0.2 1.0
CB E:CYS810 3.2 74.8 1.0
CB E:CYS813 3.7 59.0 1.0
N E:CYS813 4.2 78.7 1.0
CB E:HIS871 4.3 53.4 1.0
CZ2 E:TRP873 4.4 44.5 1.0
CA E:CYS864 4.4 80.7 1.0
NE1 E:TRP873 4.4 45.8 1.0
CA E:CYS813 4.5 72.0 1.0
CA E:CYS869 4.5 0.3 1.0
CA E:CYS810 4.7 75.7 1.0
CE2 E:TRP873 4.8 49.6 1.0
CB E:ARG866 4.8 0.6 1.0
O E:ARG866 4.8 0.5 1.0
CB E:LYS812 4.8 64.6 1.0
CB E:ALA815 4.8 57.4 1.0
N E:HIS871 5.0 70.3 1.0

Zinc binding site 4 out of 6 in 5f9f

Go back to Zinc Binding Sites List in 5f9f
Zinc binding site 4 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1001

b:0.1
occ:1.00
 SG G:CYS813 2.2 56.0 1.0
SG G:CYS810 2.3 47.2 1.0
SG G:CYS864 2.3 52.6 1.0
CB G:CYS864 2.5 63.5 1.0
SG G:CYS869 2.6 94.4 1.0
CB G:CYS810 3.2 36.4 1.0
CB G:CYS869 3.3 35.0 1.0
CB G:CYS813 3.9 53.8 1.0
CB G:HIS871 3.9 31.6 1.0
CA G:CYS864 4.0 49.6 1.0
NE1 G:TRP873 4.1 44.8 1.0
N G:CYS813 4.3 53.5 1.0
CZ2 G:TRP873 4.4 46.4 1.0
N G:HIS871 4.4 39.7 1.0
CE2 G:TRP873 4.6 39.2 1.0
CB G:LYS812 4.6 38.0 1.0
CA G:CYS810 4.7 50.0 1.0
CA G:CYS869 4.7 45.0 1.0
CA G:CYS813 4.7 46.7 1.0
C G:CYS864 4.7 43.7 1.0
N G:CYS864 4.7 52.1 1.0
CA G:HIS871 4.8 33.0 1.0
N G:SER870 4.8 49.1 1.0
C G:CYS869 5.0 43.8 1.0

Zinc binding site 5 out of 6 in 5f9f

Go back to Zinc Binding Sites List in 5f9f
Zinc binding site 5 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1001

b:0.8
occ:1.00
 SG I:CYS813 2.4 68.5 1.0
SG I:CYS869 2.4 59.0 1.0
SG I:CYS810 2.4 52.5 1.0
SG I:CYS864 2.5 72.6 1.0
CB I:CYS810 3.0 44.8 1.0
CB I:CYS864 3.1 49.1 1.0
CB I:CYS869 3.2 70.5 1.0
CB I:CYS813 3.7 57.4 1.0
N I:CYS813 3.9 54.6 1.0
CA I:CYS813 4.3 55.6 1.0
CZ2 I:TRP873 4.4 63.4 1.0
CB I:ALA815 4.4 40.7 1.0
CA I:CYS810 4.5 56.3 1.0
CB I:LYS812 4.6 39.9 1.0
CB I:HIS871 4.6 45.1 1.0
CA I:CYS864 4.6 47.1 1.0
NE1 I:TRP873 4.6 61.5 1.0
CA I:CYS869 4.7 70.1 1.0
C I:CYS813 4.8 56.2 1.0
CE2 I:TRP873 4.9 67.9 1.0
N I:ALA815 4.9 53.2 1.0
C I:LYS812 4.9 56.7 1.0
N I:LYS814 5.0 48.4 1.0

Zinc binding site 6 out of 6 in 5f9f

Go back to Zinc Binding Sites List in 5f9f
Zinc binding site 6 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn1001

b:94.4
occ:1.00
 SG K:CYS813 2.3 60.6 1.0
SG K:CYS869 2.4 79.0 1.0
SG K:CYS864 2.4 61.0 1.0
SG K:CYS810 2.5 68.5 1.0
CB K:CYS864 3.0 77.7 1.0
CB K:CYS810 3.2 39.2 1.0
CB K:CYS813 3.6 60.9 1.0
CB K:CYS869 3.7 75.3 1.0
N K:CYS813 3.9 61.2 1.0
CB K:HIS871 4.3 66.6 1.0
CA K:CYS813 4.3 64.4 1.0
CZ2 K:TRP873 4.4 56.3 1.0
NE1 K:TRP873 4.4 54.9 1.0
CB K:LYS812 4.5 59.3 1.0
CA K:CYS864 4.5 73.3 1.0
CA K:CYS810 4.7 48.8 1.0
CB K:ARG866 4.7 78.6 1.0
N K:HIS871 4.7 70.9 1.0
CE2 K:TRP873 4.7 56.3 1.0
CB K:ALA815 4.8 44.8 1.0
C K:LYS812 4.9 60.5 1.0
C K:CYS813 5.0 65.2 1.0
CA K:CYS869 5.0 73.4 1.0

Reference:

S.C.Devarkar, C.Wang, M.T.Miller, A.Ramanathan, F.Jiang, A.G.Khan, S.S.Patel, J.Marcotrigiano. Structural Basis For M7G Recognition and 2'-O-Methyl Discrimination in Capped Rnas By the Innate Immune Receptor Rig-I. Proc.Natl.Acad.Sci.Usa V. 113 596 2016.
ISSN: ESSN 1091-6490
PubMed: 26733676
DOI: 10.1073/PNAS.1515152113
Page generated: Sun Oct 27 15:54:01 2024

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