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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: Wed Dec 16 06:13:24 2020

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