Atomistry » Zinc » PDB 5f8j-5fi9 » 5f9f
Atomistry »
  Zinc »
    PDB 5f8j-5fi9 »
      5f9f »

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy