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Fluorine in PDB 4a36: Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue

Protein crystallography data

The structure of Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue, PDB code: 4a36 was solved by E.Kowalinski, T.Lunardi, A.A.Mccarthy, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.95 / 3.70
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 129.270, 129.270, 106.310, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 26.3

Other elements in 4a36:

The structure of Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue (pdb code 4a36). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue, PDB code: 4a36:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4a36

Go back to Fluorine Binding Sites List in 4a36
Fluorine binding site 1 out of 6 in the Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1796

b:35.2
occ:1.00
 F1 A:AF31796 0.0 35.2 1.0
AL A:AF31796 1.8 34.3 1.0
NZ A:LYS273 2.4 70.5 1.0
O3B A:ADP1794 2.6 63.0 1.0
F2 A:AF31796 3.0 35.8 1.0
F3 A:AF31796 3.1 39.5 1.0
CE A:LYS273 3.1 72.2 1.0
CB A:ALA412 3.3 61.1 1.0
OE1 A:GLN727 3.5 67.3 1.0
CA A:THR269 3.5 79.5 1.0
PB A:ADP1794 3.7 68.7 1.0
OG1 A:THR269 3.8 0.1 1.0
CB A:THR269 3.8 85.6 1.0
OE2 A:GLU376 4.0 85.6 1.0
OE1 A:GLU376 4.0 83.0 1.0
O2B A:ADP1794 4.0 66.5 1.0
N A:GLY270 4.1 82.0 1.0
NH2 A:ARG731 4.1 93.3 1.0
NE2 A:GLN727 4.2 68.9 1.0
CD A:GLN727 4.3 68.4 1.0
C A:THR269 4.4 76.6 1.0
O1B A:ADP1794 4.4 66.1 1.0
N A:ALA412 4.4 56.2 1.0
CD A:GLU376 4.4 82.2 1.0
N A:THR269 4.5 78.5 1.0
CA A:ALA412 4.5 60.7 1.0
NH2 A:ARG733 4.5 81.1 1.0
CD A:LYS273 4.6 74.2 1.0
MG A:MG1795 4.6 35.9 1.0
O A:PRO268 4.7 75.3 1.0
C A:PRO268 4.9 75.4 1.0

Fluorine binding site 2 out of 6 in 4a36

Go back to Fluorine Binding Sites List in 4a36
Fluorine binding site 2 out of 6 in the Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1796

b:35.8
occ:1.00
 F2 A:AF31796 0.0 35.8 1.0
AL A:AF31796 1.8 34.3 1.0
NH2 A:ARG733 2.1 81.1 1.0
O3B A:ADP1794 2.5 63.0 1.0
NH1 A:ARG731 2.9 90.5 1.0
NH2 A:ARG731 3.0 93.3 1.0
F1 A:AF31796 3.0 35.2 1.0
F3 A:AF31796 3.0 39.5 1.0
CZ A:ARG733 3.2 86.8 1.0
CZ A:ARG731 3.4 92.3 1.0
PB A:ADP1794 3.5 68.7 1.0
OG1 A:THR269 3.7 0.1 1.0
O2B A:ADP1794 3.7 66.5 1.0
NH1 A:ARG733 3.9 87.5 1.0
CA A:GLY704 4.0 80.6 1.0
O3A A:ADP1794 4.0 63.8 1.0
NE A:ARG733 4.1 93.1 1.0
C A:GLY704 4.1 81.4 1.0
O A:GLY704 4.1 80.0 1.0
N A:GLY270 4.1 82.0 1.0
N A:GLY704 4.4 83.3 1.0
MG A:MG1795 4.5 35.9 1.0
O A:GLY730 4.6 0.3 1.0
NZ A:LYS273 4.6 70.5 1.0
CA A:GLY270 4.6 85.6 1.0
CB A:THR269 4.7 85.6 1.0
OE1 A:GLN727 4.7 67.3 1.0
C A:THR269 4.7 76.6 1.0
CA A:THR269 4.7 79.5 1.0
NE A:ARG731 4.7 95.8 1.0
N A:ILE705 4.7 80.1 1.0
O2A A:ADP1794 4.8 60.9 1.0
O A:ILE705 4.9 81.7 1.0
O1B A:ADP1794 4.9 66.1 1.0
OE2 A:GLU376 5.0 85.6 1.0

Fluorine binding site 3 out of 6 in 4a36

Go back to Fluorine Binding Sites List in 4a36
Fluorine binding site 3 out of 6 in the Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1796

b:39.5
occ:1.00
 F3 A:AF31796 0.0 39.5 1.0
AL A:AF31796 1.8 34.3 1.0
MG A:MG1795 1.9 35.9 1.0
O2B A:ADP1794 2.3 66.5 1.0
OE1 A:GLU376 2.8 83.0 1.0
F2 A:AF31796 3.0 35.8 1.0
F1 A:AF31796 3.1 35.2 1.0
NZ A:LYS273 3.1 70.5 1.0
O3B A:ADP1794 3.2 63.0 1.0
CA A:GLY704 3.2 80.6 1.0
PB A:ADP1794 3.3 68.7 1.0
CD A:GLU376 3.5 82.2 1.0
OE2 A:GLU376 3.6 85.6 1.0
O A:GLY704 3.7 80.0 1.0
OD2 A:ASP375 3.8 65.1 1.0
C A:GLY704 3.9 81.4 1.0
N A:GLY704 4.1 83.3 1.0
O1B A:ADP1794 4.4 66.1 1.0
OD1 A:ASP375 4.4 67.3 1.0
CE A:LYS273 4.4 72.2 1.0
O3A A:ADP1794 4.5 63.8 1.0
CG A:ASP375 4.5 67.2 1.0
O2A A:ADP1794 4.5 60.9 1.0
CG A:GLU376 4.6 79.2 1.0
NH2 A:ARG733 4.8 81.1 1.0
NH2 A:ARG731 4.9 93.3 1.0

Fluorine binding site 4 out of 6 in 4a36

Go back to Fluorine Binding Sites List in 4a36
Fluorine binding site 4 out of 6 in the Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1796

b:40.1
occ:1.00
 F1 B:AF31796 0.0 40.1 1.0
AL B:AF31796 1.8 39.3 1.0
NZ B:LYS273 2.7 79.3 1.0
OE1 B:GLN727 3.0 73.5 1.0
F2 B:AF31796 3.0 41.7 1.0
O3B B:ADP1794 3.1 60.6 1.0
F3 B:AF31796 3.1 41.5 1.0
OE1 B:GLU376 3.3 74.2 1.0
OE2 B:GLU376 3.5 75.5 1.0
CB B:ALA412 3.5 83.7 1.0
NE2 B:GLN727 3.6 74.5 1.0
CE B:LYS273 3.7 73.9 1.0
CD B:GLN727 3.7 72.4 1.0
NH2 B:ARG731 3.8 71.6 1.0
CD B:GLU376 3.8 76.1 1.0
CA B:THR269 4.0 80.1 1.0
OG1 B:THR269 4.0 84.3 1.0
CB B:THR269 4.0 83.4 1.0
O2B B:ADP1794 4.0 69.6 1.0
PB B:ADP1794 4.1 68.3 1.0
N B:ALA412 4.3 75.0 1.0
CA B:ALA412 4.6 77.5 1.0
N B:GLY270 4.8 70.8 1.0
MG B:MG1795 4.8 35.5 1.0
N B:THR269 4.9 80.0 1.0
NH2 B:ARG733 4.9 87.2 1.0
N B:GLY704 4.9 78.9 1.0
C B:THR269 4.9 76.6 1.0
O1B B:ADP1794 4.9 67.8 1.0
CA B:GLY704 4.9 73.4 1.0
CZ B:ARG731 5.0 70.4 1.0

Fluorine binding site 5 out of 6 in 4a36

Go back to Fluorine Binding Sites List in 4a36
Fluorine binding site 5 out of 6 in the Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1796

b:41.7
occ:1.00
 F2 B:AF31796 0.0 41.7 1.0
AL B:AF31796 1.8 39.3 1.0
NH2 B:ARG733 2.2 87.2 1.0
NH2 B:ARG731 2.5 71.6 1.0
O3B B:ADP1794 2.7 60.6 1.0
NH1 B:ARG731 2.8 73.1 1.0
F1 B:AF31796 3.0 40.1 1.0
CZ B:ARG731 3.1 70.4 1.0
F3 B:AF31796 3.1 41.5 1.0
OG1 B:THR269 3.2 84.3 1.0
CZ B:ARG733 3.4 85.3 1.0
PB B:ADP1794 3.8 68.3 1.0
O2B B:ADP1794 4.0 69.6 1.0
NE B:ARG733 4.0 85.8 1.0
N B:GLY270 4.1 70.8 1.0
CA B:GLY704 4.1 73.4 1.0
CB B:THR269 4.2 83.4 1.0
NH1 B:ARG733 4.2 85.6 1.0
O B:GLY730 4.2 78.3 1.0
O3A B:ADP1794 4.2 64.7 1.0
OE1 B:GLN727 4.3 73.5 1.0
N B:GLY704 4.3 78.9 1.0
C B:GLY704 4.4 68.1 1.0
NE B:ARG731 4.4 67.1 1.0
CA B:THR269 4.4 80.1 1.0
C B:THR269 4.5 76.6 1.0
O B:GLY704 4.5 70.7 1.0
CA B:GLY270 4.7 68.3 1.0
NZ B:LYS273 4.8 79.3 1.0
N B:ILE705 4.9 61.9 1.0
C B:GLY730 4.9 79.0 1.0
O B:ILE705 4.9 64.8 1.0
OE1 B:GLU376 5.0 74.2 1.0

Fluorine binding site 6 out of 6 in 4a36

Go back to Fluorine Binding Sites List in 4a36
Fluorine binding site 6 out of 6 in the Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Duck Rig-I Helicase Domain Bound to 19-Mer Dsrna and Atp Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1796

b:41.5
occ:1.00
 F3 B:AF31796 0.0 41.5 1.0
AL B:AF31796 1.8 39.3 1.0
O2B B:ADP1794 2.3 69.6 1.0
MG B:MG1795 2.3 35.5 1.0
CA B:GLY704 2.9 73.4 1.0
OE2 B:GLU376 3.0 75.5 1.0
F2 B:AF31796 3.1 41.7 1.0
F1 B:AF31796 3.1 40.1 1.0
PB B:ADP1794 3.3 68.3 1.0
O3B B:ADP1794 3.4 60.6 1.0
O B:GLY704 3.4 70.7 1.0
C B:GLY704 3.5 68.1 1.0
CD B:GLU376 3.6 76.1 1.0
NZ B:LYS273 3.6 79.3 1.0
OE1 B:GLU376 3.7 74.2 1.0
N B:GLY704 3.8 78.9 1.0
OD2 B:ASP375 4.0 74.0 1.0
O3A B:ADP1794 4.2 64.7 1.0
O2A B:ADP1794 4.4 61.6 1.0
NH2 B:ARG733 4.5 87.2 1.0
NH2 B:ARG731 4.6 71.6 1.0
O1B B:ADP1794 4.6 67.8 1.0
NH1 B:ARG731 4.7 73.1 1.0
CG B:GLU376 4.7 75.5 1.0
N B:ILE705 4.7 61.9 1.0
CE B:LYS273 4.9 73.9 1.0
CG B:ASP375 4.9 75.7 1.0
OD1 B:ASP375 4.9 77.1 1.0
PA B:ADP1794 4.9 61.0 1.0

Reference:

E.Kowalinski, T.Lunardi, A.A.Mccarthy, J.Louber, J.Brunel, B.Grigorov, D.Gerlier, S.Cusack. Structural Basis For the Activation of Innate Immune Pattern Recognition Receptor Rig-I By Viral Rna. Cell(Cambridge,Mass.) V. 147 423 2011.
ISSN: ISSN 0092-8674
PubMed: 22000019
DOI: 10.1016/J.CELL.2011.09.039
Page generated: Wed Jul 31 23:55:51 2024

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