Atomistry » Zinc » PDB 5f8h-5fi3 » 5f9h
Atomistry »
  Zinc »
    PDB 5f8h-5fi3 »
      5f9h »

Zinc in PDB 5f9h: Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna

Enzymatic activity of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna

All present enzymatic activity of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna, PDB code: 5f9h was solved by C.Wang, J.Marcotrigiano, M.Miller, F.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.44 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.180, 174.810, 309.280, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.6

Other elements in 5f9h:

The structure of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna (pdb code 5f9h). 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 5' Triphosphate Hairpin Rna, PDB code: 5f9h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5f9h

Go back to Zinc Binding Sites List in 5f9h
Zinc binding site 1 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:75.7
occ:1.00
 SG A:CYS813 2.3 1.0 1.0
SG A:CYS869 2.4 89.0 1.0
SG A:CYS864 2.4 76.8 1.0
SG A:CYS810 2.4 62.5 1.0
CB A:CYS864 2.9 77.8 1.0
CB A:CYS810 3.1 62.7 1.0
CB A:CYS869 3.3 0.4 1.0
CB A:CYS813 3.6 95.7 1.0
N A:CYS813 3.9 87.0 1.0
NE1 A:TRP873 4.3 84.3 1.0
CB A:HIS871 4.3 60.2 1.0
CZ2 A:TRP873 4.3 92.0 1.0
CA A:CYS813 4.3 91.0 1.0
CA A:CYS864 4.4 79.8 1.0
CA A:CYS810 4.6 61.8 1.0
CE2 A:TRP873 4.6 88.2 1.0
CB A:LYS812 4.7 75.6 1.0
CA A:CYS869 4.7 0.3 1.0
CB A:ALA815 4.9 80.1 1.0
C A:CYS813 4.9 86.1 1.0

Zinc binding site 2 out of 6 in 5f9h

Go back to Zinc Binding Sites List in 5f9h
Zinc binding site 2 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:74.2
occ:1.00
 SG C:CYS813 2.2 77.5 1.0
SG C:CYS869 2.3 60.0 1.0
SG C:CYS810 2.3 61.4 1.0
SG C:CYS864 2.3 67.0 1.0
CB C:CYS864 3.0 71.5 1.0
CB C:CYS869 3.1 66.2 1.0
CB C:CYS810 3.1 46.6 1.0
CB C:CYS813 3.5 79.3 1.0
N C:CYS813 3.8 73.1 1.0
CA C:CYS813 4.2 73.7 1.0
CB C:HIS871 4.3 49.1 1.0
NE1 C:TRP873 4.5 70.8 1.0
CA C:CYS864 4.5 71.1 1.0
CA C:CYS869 4.5 70.8 1.0
CB C:LYS812 4.5 56.5 1.0
CZ2 C:TRP873 4.6 73.6 1.0
CA C:CYS810 4.6 49.7 1.0
C C:CYS813 4.9 69.5 1.0
CB C:ALA815 4.9 62.6 1.0
CE2 C:TRP873 4.9 71.7 1.0
C C:LYS812 4.9 67.2 1.0
N C:HIS871 4.9 50.5 1.0
C C:CYS869 4.9 65.7 1.0

Zinc binding site 3 out of 6 in 5f9h

Go back to Zinc Binding Sites List in 5f9h
Zinc binding site 3 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:82.3
occ:1.00
 SG E:CYS813 2.2 59.5 1.0
SG E:CYS864 2.4 72.4 1.0
SG E:CYS869 2.4 70.7 1.0
SG E:CYS810 2.5 84.1 1.0
CB E:CYS864 2.9 69.3 1.0
CB E:CYS869 3.4 0.9 1.0
CB E:CYS810 3.4 82.2 1.0
CB E:CYS813 3.6 67.5 1.0
N E:CYS813 4.0 70.5 1.0
CB E:HIS871 4.4 71.3 1.0
CA E:CYS813 4.4 67.4 1.0
CA E:CYS864 4.4 73.6 1.0
CB E:ARG866 4.5 0.8 1.0
N E:HIS871 4.6 84.4 1.0
CZ2 E:TRP873 4.6 71.7 1.0
NE1 E:TRP873 4.6 67.1 1.0
CB E:LYS812 4.6 65.1 1.0
N E:SER870 4.7 0.6 1.0
CA E:CYS869 4.7 0.9 1.0
CB E:ALA815 4.7 58.6 1.0
CA E:CYS810 4.8 86.2 1.0
C E:CYS869 4.8 0.2 1.0
CE2 E:TRP873 4.9 68.8 1.0

Zinc binding site 4 out of 6 in 5f9h

Go back to Zinc Binding Sites List in 5f9h
Zinc binding site 4 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1001

b:77.6
occ:1.00
 SG G:CYS810 2.3 45.1 1.0
SG G:CYS813 2.3 0.7 1.0
SG G:CYS869 2.3 67.9 1.0
SG G:CYS864 2.4 1.0 1.0
CB G:CYS864 2.9 53.7 1.0
CB G:CYS869 3.0 60.0 1.0
CB G:CYS810 3.2 45.8 1.0
CB G:CYS813 3.5 83.9 1.0
N G:CYS813 3.9 87.6 1.0
CA G:CYS813 4.3 85.6 1.0
CZ2 G:TRP873 4.3 66.0 1.0
NE1 G:TRP873 4.4 68.1 1.0
CA G:CYS864 4.4 51.5 1.0
CB G:HIS871 4.4 47.3 1.0
CA G:CYS869 4.5 65.5 1.0
CB G:LYS812 4.5 45.6 1.0
CA G:CYS810 4.6 53.2 1.0
CE2 G:TRP873 4.7 67.9 1.0
C G:CYS869 4.9 67.1 1.0
CB G:ALA815 4.9 71.0 1.0
N G:HIS871 4.9 53.7 1.0
C G:LYS812 5.0 68.6 1.0
C G:CYS813 5.0 86.4 1.0

Zinc binding site 5 out of 6 in 5f9h

Go back to Zinc Binding Sites List in 5f9h
Zinc binding site 5 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1001

b:74.7
occ:1.00
 SG I:CYS813 2.3 0.8 1.0
SG I:CYS810 2.4 74.0 1.0
SG I:CYS864 2.5 77.1 1.0
SG I:CYS869 2.9 78.0 1.0
CB I:CYS864 3.1 93.8 1.0
CB I:CYS810 3.4 60.0 1.0
CB I:CYS813 3.5 0.1 1.0
N I:CYS813 3.7 0.7 1.0
CB I:LYS812 4.1 74.5 1.0
CA I:CYS813 4.2 0.4 1.0
CB I:HIS871 4.3 75.2 1.0
NE1 I:TRP873 4.5 84.6 1.0
CB I:CYS869 4.6 0.8 1.0
CA I:CYS864 4.7 90.8 1.0
CZ2 I:TRP873 4.7 92.8 1.0
C I:LYS812 4.7 98.0 1.0
CA I:LYS812 4.8 82.3 1.0
CA I:CYS810 4.8 68.6 1.0
N I:LYS812 4.9 76.9 1.0
CG I:LYS812 4.9 70.2 1.0
CE2 I:TRP873 5.0 88.2 1.0
CD I:LYS812 5.0 67.1 1.0

Zinc binding site 6 out of 6 in 5f9h

Go back to Zinc Binding Sites List in 5f9h
Zinc binding site 6 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn1001

b:75.5
occ:1.00
 SG K:CYS813 2.2 56.5 1.0
SG K:CYS864 2.3 57.7 1.0
SG K:CYS869 2.5 79.8 1.0
SG K:CYS810 2.5 80.1 1.0
CB K:CYS864 2.9 60.3 1.0
CB K:CYS810 3.2 54.4 1.0
CB K:CYS869 3.4 98.4 1.0
CB K:CYS813 3.6 69.6 1.0
N K:CYS813 4.0 68.0 1.0
CB K:HIS871 4.2 62.5 1.0
CZ2 K:TRP873 4.3 59.7 1.0
CA K:CYS813 4.4 67.8 1.0
CA K:CYS864 4.4 66.7 1.0
NE1 K:TRP873 4.5 54.7 1.0
N K:HIS871 4.6 71.4 1.0
CA K:CYS810 4.7 54.1 1.0
CE2 K:TRP873 4.7 55.7 1.0
CB K:LYS812 4.7 77.5 1.0
CA K:CYS869 4.8 99.9 1.0
CB K:ARG866 4.8 0.4 1.0
CB K:ALA815 4.9 56.5 1.0
N K:SER870 4.9 94.9 1.0
CG K:ARG866 5.0 96.0 1.0
C K:CYS869 5.0 89.6 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 15:54:58 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy