Fluorine in PDB 7jl2: Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)

Enzymatic activity of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)

All present enzymatic activity of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer):
3.6.4.13;

Other elements in 7jl2:

The structure of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Aluminium (Al) 3 atoms
Zinc (Zn) 3 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) (pdb code 7jl2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer), PDB code: 7jl2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 7jl2

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Fluorine binding site 1 out of 12 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1103

b:73.5
occ:1.00
 F1 A:ALF1103 0.0 73.5 1.0
AL A:ALF1103 1.8 73.5 1.0
MG A:MG1104 1.9 59.3 1.0
F4 A:ALF1103 2.5 73.5 1.0
F3 A:ALF1103 2.5 73.5 1.0
O1B A:ADP1102 3.0 73.6 1.0
CA A:GLY795 3.2 61.3 1.0
F2 A:ALF1103 3.6 73.5 1.0
N A:GLY795 3.7 61.3 1.0
O2B A:ADP1102 3.8 73.6 1.0
PB A:ADP1102 3.9 73.6 1.0
C A:GLY795 4.0 61.3 1.0
O A:GLY795 4.2 61.3 1.0
NH2 A:ARG822 4.3 95.0 1.0
OE2 A:GLU444 4.4 95.0 1.0
O3A A:ADP1102 4.5 73.6 1.0
C A:GLU794 4.5 62.0 1.0
NH1 A:ARG822 4.7 95.0 1.0
NH2 A:ARG824 4.8 95.0 1.0
CZ A:ARG822 4.9 95.0 1.0
N A:LEU796 4.9 69.2 1.0
OE1 A:GLN818 5.0 95.0 1.0

Fluorine binding site 2 out of 12 in 7jl2

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Fluorine binding site 2 out of 12 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1103

b:73.5
occ:1.00
 F2 A:ALF1103 0.0 73.5 1.0
AL A:ALF1103 1.8 73.5 1.0
O2B A:ADP1102 2.1 73.6 1.0
NZ A:LYS335 2.2 95.0 1.0
F3 A:ALF1103 2.5 73.5 1.0
F4 A:ALF1103 2.5 73.5 1.0
PB A:ADP1102 3.0 73.6 1.0
CE A:LYS335 3.2 95.0 1.0
O1B A:ADP1102 3.3 73.6 1.0
F1 A:ALF1103 3.6 73.5 1.0
CA A:THR331 3.7 95.0 1.0
O3B A:ADP1102 3.7 73.6 1.0
CG2 A:THR331 4.0 95.0 1.0
MG A:MG1104 4.0 59.3 1.0
CB A:THR331 4.0 95.0 1.0
N A:GLY332 4.1 95.0 1.0
O3A A:ADP1102 4.4 73.6 1.0
CB A:ALA489 4.4 95.0 1.0
C A:THR331 4.5 95.0 1.0
CD A:LYS335 4.5 95.0 1.0
NH2 A:ARG824 4.6 95.0 1.0
N A:THR331 4.7 95.0 1.0
OE1 A:GLN818 4.9 95.0 1.0

Fluorine binding site 3 out of 12 in 7jl2

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Fluorine binding site 3 out of 12 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1103

b:73.5
occ:1.00
 F3 A:ALF1103 0.0 73.5 1.0
AL A:ALF1103 1.8 73.5 1.0
F2 A:ALF1103 2.5 73.5 1.0
F1 A:ALF1103 2.5 73.5 1.0
O2B A:ADP1102 2.7 73.6 1.0
NH2 A:ARG822 3.1 95.0 1.0
NH2 A:ARG824 3.3 95.0 1.0
NH1 A:ARG822 3.5 95.0 1.0
F4 A:ALF1103 3.6 73.5 1.0
CZ A:ARG822 3.8 95.0 1.0
PB A:ADP1102 3.8 73.6 1.0
O1B A:ADP1102 3.9 73.6 1.0
MG A:MG1104 3.9 59.3 1.0
OE1 A:GLN818 4.0 95.0 1.0
CB A:THR331 4.2 95.0 1.0
CG2 A:THR331 4.3 95.0 1.0
O3A A:ADP1102 4.4 73.6 1.0
CZ A:ARG824 4.5 95.0 1.0
N A:GLY332 4.5 95.0 1.0
CA A:THR331 4.6 95.0 1.0
NZ A:LYS335 4.7 95.0 1.0
N A:GLY795 4.8 61.3 1.0
CA A:GLY795 4.9 61.3 1.0

Fluorine binding site 4 out of 12 in 7jl2

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Fluorine binding site 4 out of 12 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1103

b:73.5
occ:1.00
 F4 A:ALF1103 0.0 73.5 1.0
AL A:ALF1103 1.8 73.5 1.0
MG A:MG1104 1.9 59.3 1.0
O1B A:ADP1102 2.2 73.6 1.0
F1 A:ALF1103 2.5 73.5 1.0
F2 A:ALF1103 2.5 73.5 1.0
PB A:ADP1102 3.1 73.6 1.0
CE A:LYS335 3.1 95.0 1.0
NZ A:LYS335 3.2 95.0 1.0
O2B A:ADP1102 3.3 73.6 1.0
F3 A:ALF1103 3.6 73.5 1.0
O3B A:ADP1102 3.9 73.6 1.0
O3A A:ADP1102 4.4 73.6 1.0
CD A:LYS335 4.6 95.0 1.0
OD1 A:ASP443 4.7 95.0 1.0
O2A A:ADP1102 4.9 73.6 1.0
CB A:LYS335 5.0 95.0 1.0

Fluorine binding site 5 out of 12 in 7jl2

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Fluorine binding site 5 out of 12 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1103

b:88.8
occ:1.00
 F1 C:ALF1103 0.0 88.8 1.0
AL C:ALF1103 1.8 88.8 1.0
MG C:MG1104 1.9 87.2 1.0
F4 C:ALF1103 2.5 88.8 1.0
F3 C:ALF1103 2.5 88.8 1.0
O1B C:ADP1102 3.0 85.8 1.0
CA C:GLY795 3.2 70.9 1.0
F2 C:ALF1103 3.6 88.8 1.0
N C:GLY795 3.7 70.9 1.0
O2B C:ADP1102 3.8 85.8 1.0
PB C:ADP1102 3.9 85.8 1.0
C C:GLY795 4.0 70.9 1.0
O C:GLY795 4.2 70.9 1.0
NH2 C:ARG822 4.3 95.0 1.0
OE2 C:GLU444 4.4 95.0 1.0
O3A C:ADP1102 4.5 85.8 1.0
C C:GLU794 4.5 71.6 1.0
NH1 C:ARG822 4.7 95.0 1.0
NH2 C:ARG824 4.8 95.0 1.0
CZ C:ARG822 4.9 95.0 1.0
N C:LEU796 4.9 77.9 1.0
OE1 C:GLN818 5.0 95.0 1.0

Fluorine binding site 6 out of 12 in 7jl2

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Fluorine binding site 6 out of 12 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1103

b:88.8
occ:1.00
 F2 C:ALF1103 0.0 88.8 1.0
AL C:ALF1103 1.8 88.8 1.0
O2B C:ADP1102 2.1 85.8 1.0
NZ C:LYS335 2.2 95.0 1.0
F3 C:ALF1103 2.5 88.8 1.0
F4 C:ALF1103 2.5 88.8 1.0
PB C:ADP1102 3.0 85.8 1.0
CE C:LYS335 3.2 95.0 1.0
O1B C:ADP1102 3.3 85.8 1.0
F1 C:ALF1103 3.6 88.8 1.0
CA C:THR331 3.7 95.0 1.0
O3B C:ADP1102 3.7 85.8 1.0
CG2 C:THR331 4.0 95.0 1.0
MG C:MG1104 4.0 87.2 1.0
CB C:THR331 4.0 95.0 1.0
N C:GLY332 4.1 95.0 1.0
O3A C:ADP1102 4.4 85.8 1.0
CB C:ALA489 4.4 95.0 1.0
C C:THR331 4.5 95.0 1.0
CD C:LYS335 4.5 95.0 1.0
NH2 C:ARG824 4.6 95.0 1.0
N C:THR331 4.7 95.0 1.0
OE1 C:GLN818 4.9 95.0 1.0

Fluorine binding site 7 out of 12 in 7jl2

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Fluorine binding site 7 out of 12 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1103

b:88.8
occ:1.00
 F3 C:ALF1103 0.0 88.8 1.0
AL C:ALF1103 1.8 88.8 1.0
F2 C:ALF1103 2.5 88.8 1.0
F1 C:ALF1103 2.5 88.8 1.0
O2B C:ADP1102 2.7 85.8 1.0
NH2 C:ARG822 3.1 95.0 1.0
NH2 C:ARG824 3.3 95.0 1.0
NH1 C:ARG822 3.5 95.0 1.0
F4 C:ALF1103 3.6 88.8 1.0
CZ C:ARG822 3.8 95.0 1.0
PB C:ADP1102 3.8 85.8 1.0
O1B C:ADP1102 3.9 85.8 1.0
MG C:MG1104 3.9 87.2 1.0
OE1 C:GLN818 4.0 95.0 1.0
CB C:THR331 4.2 95.0 1.0
CG2 C:THR331 4.3 95.0 1.0
O3A C:ADP1102 4.4 85.8 1.0
CZ C:ARG824 4.5 95.0 1.0
N C:GLY332 4.5 95.0 1.0
CA C:THR331 4.6 95.0 1.0
NZ C:LYS335 4.7 95.0 1.0
N C:GLY795 4.8 70.9 1.0
CA C:GLY795 4.9 70.9 1.0

Fluorine binding site 8 out of 12 in 7jl2

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Fluorine binding site 8 out of 12 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1103

b:88.8
occ:1.00
 F4 C:ALF1103 0.0 88.8 1.0
AL C:ALF1103 1.8 88.8 1.0
MG C:MG1104 1.9 87.2 1.0
O1B C:ADP1102 2.2 85.8 1.0
F1 C:ALF1103 2.5 88.8 1.0
F2 C:ALF1103 2.5 88.8 1.0
PB C:ADP1102 3.1 85.8 1.0
CE C:LYS335 3.1 95.0 1.0
NZ C:LYS335 3.2 95.0 1.0
O2B C:ADP1102 3.3 85.8 1.0
F3 C:ALF1103 3.6 88.8 1.0
O3B C:ADP1102 3.9 85.8 1.0
O3A C:ADP1102 4.4 85.8 1.0
CD C:LYS335 4.6 95.0 1.0
OD1 C:ASP443 4.7 95.0 1.0
O2A C:ADP1102 4.9 85.8 1.0
CB C:LYS335 5.0 95.0 1.0

Fluorine binding site 9 out of 12 in 7jl2

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Fluorine binding site 9 out of 12 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1103

b:75.0
occ:1.00
 F1 E:ALF1103 0.0 75.0 1.0
AL E:ALF1103 1.8 75.0 1.0
MG E:MG1104 1.9 66.8 1.0
F4 E:ALF1103 2.5 75.0 1.0
F3 E:ALF1103 2.5 75.0 1.0
O1B E:ADP1102 3.0 76.2 1.0
CA E:GLY795 3.2 61.8 1.0
F2 E:ALF1103 3.6 75.0 1.0
N E:GLY795 3.7 61.8 1.0
O2B E:ADP1102 3.8 76.2 1.0
PB E:ADP1102 3.9 76.2 1.0
C E:GLY795 4.0 61.8 1.0
O E:GLY795 4.2 61.8 1.0
NH2 E:ARG822 4.3 95.0 1.0
OE2 E:GLU444 4.4 95.0 1.0
O3A E:ADP1102 4.5 76.2 1.0
C E:GLU794 4.5 53.1 1.0
NH1 E:ARG822 4.7 95.0 1.0
NH2 E:ARG824 4.8 95.0 1.0
CZ E:ARG822 4.9 95.0 1.0
N E:LEU796 4.9 70.3 1.0
OE1 E:GLN818 5.0 95.0 1.0

Fluorine binding site 10 out of 12 in 7jl2

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Fluorine binding site 10 out of 12 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1103

b:75.0
occ:1.00
 F2 E:ALF1103 0.0 75.0 1.0
AL E:ALF1103 1.8 75.0 1.0
O2B E:ADP1102 2.1 76.2 1.0
NZ E:LYS335 2.2 95.0 1.0
F3 E:ALF1103 2.5 75.0 1.0
F4 E:ALF1103 2.5 75.0 1.0
PB E:ADP1102 3.0 76.2 1.0
CE E:LYS335 3.2 95.0 1.0
O1B E:ADP1102 3.3 76.2 1.0
F1 E:ALF1103 3.6 75.0 1.0
CA E:THR331 3.7 95.0 1.0
O3B E:ADP1102 3.7 76.2 1.0
CG2 E:THR331 4.0 95.0 1.0
MG E:MG1104 4.0 66.8 1.0
CB E:THR331 4.0 95.0 1.0
N E:GLY332 4.1 95.0 1.0
O3A E:ADP1102 4.4 76.2 1.0
CB E:ALA489 4.4 95.0 1.0
C E:THR331 4.5 95.0 1.0
CD E:LYS335 4.5 95.0 1.0
NH2 E:ARG824 4.6 95.0 1.0
N E:THR331 4.7 95.0 1.0
OE1 E:GLN818 4.9 95.0 1.0

Reference:

K.Kato, S.Ahmad, Z.Zhu, J.M.Young, X.Mu, S.Park, H.S.Malik, S.Hur. Structural Analysis of Rig-I-Like Receptors Reveals Ancient Rules of Engagement Between Diverse Rna Helicases and Trim Ubiquitin Ligases Mol.Cell 2020.
ISSN: ISSN 1097-2765
Page generated: Fri Aug 2 07:50:09 2024

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