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Fluorine 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:

Magnesium (Mg) 6 atoms
Zinc (Zn) 6 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 12 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5f9f

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Fluorine binding site 1 out of 12 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 Fluorine with other atoms in the F 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:F1003

b:37.9
occ:1.00
 F1 A:ETF1003 0.0 37.9 1.0
C1 A:ETF1003 1.3 69.4 1.0
F2 A:ETF1003 2.2 82.5 1.0
F3 A:ETF1003 2.2 80.7 1.0
C2 A:ETF1003 2.3 70.8 1.0
CB A:LYS270 3.2 35.5 1.0
CA A:LYS270 3.5 34.1 1.0
O A:ETF1003 3.5 56.6 1.0
SG A:CYS268 3.8 49.0 1.0
CG2 A:ILE262 4.0 24.3 1.0
CB A:ALA264 4.2 34.7 1.0
N A:LYS270 4.2 18.9 1.0
CG2 A:VAL273 4.3 19.5 1.0
CD1 A:LEU250 4.5 26.9 1.0
CG A:LYS270 4.7 33.4 1.0
CB A:VAL273 4.7 26.4 1.0
C A:GLY269 4.8 22.6 1.0
C A:LYS270 4.8 31.6 1.0
O A:GLY269 4.8 32.7 1.0
O A:LYS270 4.9 44.4 1.0
CD2 A:LEU408 4.9 24.7 1.0
CB A:ILE262 5.0 21.1 1.0

Fluorine binding site 2 out of 12 in 5f9f

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Fluorine binding site 2 out of 12 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 Fluorine with other atoms in the F 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
A:F1003

b:82.5
occ:1.00
 F2 A:ETF1003 0.0 82.5 1.0
C1 A:ETF1003 1.3 69.4 1.0
F1 A:ETF1003 2.2 37.9 1.0
F3 A:ETF1003 2.2 80.7 1.0
C2 A:ETF1003 2.3 70.8 1.0
O A:ETF1003 2.9 56.6 1.0
N A:ALA264 3.3 23.3 1.0
O A:ILE262 3.3 24.4 1.0
CG2 A:ILE262 3.3 24.3 1.0
CB A:ALA264 3.3 34.7 1.0
O A:THR409 3.3 28.0 1.0
C A:ILE262 3.7 23.2 1.0
CA A:ALA264 3.8 29.0 1.0
C A:CYS263 3.9 26.6 1.0
O A:ALA264 4.0 26.7 1.0
N A:CYS263 4.0 24.5 1.0
CB A:ILE262 4.0 21.1 1.0
CA A:CYS263 4.1 22.7 1.0
C A:ALA264 4.3 28.5 1.0
N A:THR409 4.3 27.9 1.0
C A:THR409 4.4 21.2 1.0
CA A:ILE262 4.5 18.9 1.0
SG A:CYS268 4.7 49.0 1.0
O A:CYS263 4.8 38.6 1.0
CD1 A:LEU250 4.8 26.9 1.0
CB A:LYS270 4.9 35.5 1.0
CA A:THR409 5.0 14.6 1.0

Fluorine binding site 3 out of 12 in 5f9f

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Fluorine binding site 3 out of 12 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 Fluorine with other atoms in the F 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
A:F1003

b:80.7
occ:1.00
 F3 A:ETF1003 0.0 80.7 1.0
C1 A:ETF1003 1.3 69.4 1.0
F2 A:ETF1003 2.2 82.5 1.0
F1 A:ETF1003 2.2 37.9 1.0
C2 A:ETF1003 2.3 70.8 1.0
O A:ETF1003 2.6 56.6 1.0
CB A:LYS270 3.2 35.5 1.0
CB A:LEU408 3.6 8.2 1.0
CD2 A:LEU408 3.8 24.7 1.0
CD A:LYS270 3.9 24.0 1.0
N A:THR409 3.9 27.9 1.0
CA A:LEU408 4.0 17.4 1.0
O A:THR409 4.1 28.0 1.0
O A:ILE262 4.1 24.4 1.0
CG A:LEU408 4.2 26.0 1.0
CG A:LYS270 4.2 33.4 1.0
C A:LEU408 4.2 19.6 1.0
CA A:LYS270 4.2 34.1 1.0
CG2 A:ILE262 4.5 24.3 1.0
CD1 A:LEU408 4.5 24.4 1.0
C A:THR409 4.7 21.2 1.0
CA A:THR409 4.7 14.6 1.0
CB A:ILE262 4.8 21.1 1.0
C A:ILE262 4.9 23.2 1.0

Fluorine binding site 4 out of 12 in 5f9f

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Fluorine binding site 4 out of 12 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 Fluorine with other atoms in the F 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
E:F1002

b:0.2
occ:1.00
 F1 E:ETF1002 0.0 0.2 1.0
C1 E:ETF1002 1.3 0.9 1.0
F3 E:ETF1002 2.2 0.2 1.0
F2 E:ETF1002 2.2 0.1 1.0
C2 E:ETF1002 2.3 75.1 1.0
NZ E:LYS888 2.6 66.2 1.0
O E:ETF1002 3.5 50.4 1.0
CE E:LYS888 4.0 48.5 1.0
OE2 E:GLU890 4.4 81.8 1.0
OD2 E:ASP872 4.6 71.6 1.0
CD E:LYS888 4.6 44.5 1.0
CD E:LYS666 4.7 52.4 1.0
NE2 E:GLN669 4.9 0.3 1.0

Fluorine binding site 5 out of 12 in 5f9f

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Fluorine binding site 5 out of 12 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 Fluorine with other atoms in the F 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
E:F1002

b:0.1
occ:1.00
 F2 E:ETF1002 0.0 0.1 1.0
C1 E:ETF1002 1.3 0.9 1.0
F3 E:ETF1002 2.2 0.2 1.0
F1 E:ETF1002 2.2 0.2 1.0
C2 E:ETF1002 2.3 75.1 1.0
O E:ETF1002 2.6 50.4 1.0
CD E:LYS666 3.2 52.4 1.0
CG E:GLN669 3.6 82.0 1.0
CB E:LYS666 3.6 49.2 1.0
CD E:GLN669 3.7 0.6 1.0
NE2 E:GLN669 3.9 0.3 1.0
CG E:LYS666 4.0 40.5 1.0
CB E:GLN669 4.3 69.0 1.0
OE1 E:GLN669 4.3 0.4 1.0
CE E:LYS666 4.4 50.9 1.0
NZ E:LYS666 4.5 53.5 1.0
C E:ASN668 4.5 57.6 1.0
O E:ASN668 4.5 62.2 1.0
NZ E:LYS888 4.5 66.2 1.0
CB E:ASN668 4.6 49.4 1.0
N E:GLN669 4.7 55.1 1.0
N E:ASN668 4.8 60.3 1.0
CA E:ASN668 4.9 54.5 1.0
CA E:LYS666 5.0 59.0 1.0

Fluorine binding site 6 out of 12 in 5f9f

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Fluorine binding site 6 out of 12 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 Fluorine with other atoms in the F 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
E:F1002

b:0.2
occ:1.00
 F3 E:ETF1002 0.0 0.2 1.0
C1 E:ETF1002 1.3 0.9 1.0
F2 E:ETF1002 2.2 0.1 1.0
F1 E:ETF1002 2.2 0.2 1.0
C2 E:ETF1002 2.3 75.1 1.0
O E:ETF1002 2.9 50.4 1.0
NZ E:LYS888 3.1 66.2 1.0
CB E:ASN668 3.3 49.4 1.0
OD2 E:ASP872 3.4 71.6 1.0
O E:ASN668 3.5 62.2 1.0
C E:ASN668 3.9 57.6 1.0
CG E:GLN669 4.1 82.0 1.0
CA E:ASN668 4.2 54.5 1.0
ND2 E:ASN668 4.3 52.7 1.0
CG E:ASP872 4.3 73.4 1.0
CG E:ASN668 4.4 49.5 1.0
CE E:LYS888 4.5 48.5 1.0
N E:GLN669 4.7 55.1 1.0
N E:ASN668 4.7 60.3 1.0
OD1 E:ASP872 4.8 79.8 1.0
NE2 E:GLN669 4.8 0.3 1.0
CD E:GLN669 4.8 0.6 1.0

Fluorine binding site 7 out of 12 in 5f9f

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Fluorine binding site 7 out of 12 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 Fluorine with other atoms in the F binding site number 7 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:F1002

b:86.2
occ:1.00
 F1 G:ETF1002 0.0 86.2 1.0
C1 G:ETF1002 1.3 83.5 1.0
F3 G:ETF1002 2.2 90.1 1.0
F2 G:ETF1002 2.2 0.8 1.0
C2 G:ETF1002 2.3 51.0 1.0
CA K:ILE337 3.3 44.4 1.0
ND2 G:ASN340 3.5 39.6 1.0
O G:ETF1002 3.5 50.6 1.0
CG1 K:ILE337 3.6 41.2 1.0
ND2 K:ASN340 3.6 25.8 1.0
N K:ILE337 3.6 41.3 1.0
O K:GLN336 3.6 38.0 1.0
C K:GLN336 3.8 43.2 1.0
CB K:ILE337 3.9 44.7 1.0
CB K:ASN340 4.0 33.5 1.0
CB G:ASN340 4.0 45.1 1.0
CG K:ASN340 4.2 28.8 1.0
CG G:ASN340 4.3 50.7 1.0
C K:ILE337 4.4 46.5 1.0
OD1 K:ASN341 4.5 39.0 1.0
O K:ILE337 4.5 54.3 1.0
CG2 K:ILE337 4.5 40.5 1.0
CG K:GLN336 4.6 54.4 1.0
O G:GLN336 4.6 34.6 1.0
CB K:GLN336 4.7 47.7 1.0
CD1 K:ILE337 4.9 51.4 1.0
CA G:ILE337 4.9 27.8 1.0
CA K:GLN336 4.9 48.3 1.0

Fluorine binding site 8 out of 12 in 5f9f

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Fluorine binding site 8 out of 12 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 Fluorine with other atoms in the F binding site number 8 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:F1002

b:0.8
occ:1.00
 F2 G:ETF1002 0.0 0.8 1.0
C1 G:ETF1002 1.3 83.5 1.0
F3 G:ETF1002 2.2 90.1 1.0
F1 G:ETF1002 2.2 86.2 1.0
C2 G:ETF1002 2.3 51.0 1.0
O G:ETF1002 2.6 50.6 1.0
ND2 G:ASN341 2.9 35.2 1.0
CB G:ASN340 3.1 45.1 1.0
CA G:ILE337 3.6 27.8 1.0
O G:GLN336 3.7 34.6 1.0
O G:ILE337 3.8 53.6 1.0
ND2 G:ASN340 3.8 39.6 1.0
CG G:ASN341 4.0 40.7 1.0
CG G:ASN340 4.0 50.7 1.0
CA G:ASN340 4.0 51.7 1.0
C G:ASN340 4.1 51.5 1.0
O G:ASN340 4.1 40.5 1.0
C G:ILE337 4.1 46.5 1.0
NH1 G:ARG320 4.3 76.6 1.0
N G:ILE337 4.3 35.4 1.0
C G:GLN336 4.3 39.6 1.0
N G:ASN340 4.4 50.1 1.0
OD1 G:ASN341 4.4 42.1 1.0
CG1 K:ILE337 4.5 41.2 1.0
CB G:ILE337 4.5 28.9 1.0
N G:ASN341 4.6 48.9 1.0
CG2 G:ILE337 4.7 24.3 1.0
CG1 G:ILE337 4.7 33.8 1.0

Fluorine binding site 9 out of 12 in 5f9f

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Fluorine binding site 9 out of 12 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 Fluorine with other atoms in the F binding site number 9 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:F1002

b:90.1
occ:1.00
 F3 G:ETF1002 0.0 90.1 1.0
C1 G:ETF1002 1.3 83.5 1.0
F2 G:ETF1002 2.2 0.8 1.0
F1 G:ETF1002 2.2 86.2 1.0
C2 G:ETF1002 2.3 51.0 1.0
O G:ETF1002 3.0 50.6 1.0
CG1 G:ILE337 3.2 33.8 1.0
CA G:ILE337 3.4 27.8 1.0
CB K:ASN340 3.6 33.5 1.0
CB G:ILE337 3.7 28.9 1.0
ND2 K:ASN340 3.8 25.8 1.0
N G:ILE337 4.0 35.4 1.0
CG2 G:ILE337 4.0 24.3 1.0
OD1 K:ASN341 4.2 39.0 1.0
ND2 G:ASN341 4.2 35.2 1.0
CG K:ASN340 4.3 28.8 1.0
CD1 G:ILE337 4.3 45.0 1.0
O G:GLN336 4.4 34.6 1.0
C G:GLN336 4.4 39.6 1.0
O K:ASN340 4.5 50.3 1.0
C G:ILE337 4.6 46.5 1.0
NH1 K:ARG320 4.6 46.7 1.0
O G:ILE337 4.7 53.6 1.0
ND2 G:ASN340 4.8 39.6 1.0
CA K:ASN340 4.9 35.4 1.0
C K:ASN340 5.0 38.4 1.0
CA K:ILE337 5.0 44.4 1.0
O K:GLN336 5.0 38.0 1.0
CB G:ASN340 5.0 45.1 1.0

Fluorine binding site 10 out of 12 in 5f9f

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Fluorine binding site 10 out of 12 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 Fluorine with other atoms in the F binding site number 10 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:F1003

b:0.6
occ:1.00
 F1 K:ETF1003 0.0 0.6 1.0
C1 K:ETF1003 1.3 0.4 1.0
F3 K:ETF1003 2.2 0.4 1.0
F2 K:ETF1003 2.2 0.5 1.0
C2 K:ETF1003 2.3 95.9 1.0
O K:ETF1003 2.8 85.6 1.0
NZ K:LYS458 3.0 55.2 1.0
CE K:LYS458 3.2 46.5 1.0
O K:MET724 3.8 51.8 1.0
SG K:CYS738 4.1 54.8 1.0
CG K:ARG728 4.4 36.4 1.0
CB K:THR727 4.5 39.6 1.0
CG K:MET724 4.5 26.9 1.0
CB K:CYS738 4.5 24.1 1.0
N K:ARG728 4.7 38.5 1.0
C K:MET724 4.7 43.6 1.0
CD K:LYS458 4.8 53.2 1.0
CG2 K:THR727 4.8 52.7 1.0
C K:THR727 4.9 40.5 1.0
OE2 K:GLU751 4.9 58.2 1.0
CA K:ARG728 5.0 31.2 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: Thu Aug 1 09:20:08 2024

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