Fluorine in PDB 7jl0: Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)
Enzymatic activity of Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)
All present enzymatic activity of Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer):
3.6.4.13;
Other elements in 7jl0:
The structure of Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer) also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)
(pdb code 7jl0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer), PDB code: 7jl0:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 7jl0
Go back to
Fluorine Binding Sites List in 7jl0
Fluorine binding site 1 out
of 4 in the Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)
![](/pictures/F/pdb/jl/7jl0-F-sphere_01.jpg) Mono view
![](/pictures/F/pdb/jl/7jl0-F-sphere_01_stereo.jpg) 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 in Complex with TRIM65 Pspry Domain (Monomer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1103
b:43.8
occ:1.00
|
F1
|
A:ALF1103
|
0.0
|
43.8
|
1.0
|
AL
|
A:ALF1103
|
1.8
|
43.8
|
1.0
|
O1B
|
A:ADP1102
|
2.1
|
48.0
|
1.0
|
MG
|
A:MG1104
|
2.1
|
24.6
|
1.0
|
F4
|
A:ALF1103
|
2.5
|
43.8
|
1.0
|
F3
|
A:ALF1103
|
2.6
|
43.8
|
1.0
|
PB
|
A:ADP1102
|
3.1
|
48.0
|
1.0
|
O2B
|
A:ADP1102
|
3.3
|
48.0
|
1.0
|
F2
|
A:ALF1103
|
3.6
|
43.8
|
1.0
|
CA
|
A:GLY795
|
3.9
|
42.1
|
1.0
|
NH1
|
A:ARG822
|
4.0
|
48.5
|
1.0
|
O3B
|
A:ADP1102
|
4.1
|
48.0
|
1.0
|
OE2
|
A:GLU444
|
4.2
|
48.5
|
1.0
|
N
|
A:GLY795
|
4.3
|
42.1
|
1.0
|
O3A
|
A:ADP1102
|
4.3
|
48.0
|
1.0
|
O
|
A:GLY795
|
4.4
|
42.1
|
1.0
|
NH2
|
A:ARG822
|
4.4
|
48.5
|
1.0
|
C
|
A:GLY795
|
4.5
|
42.1
|
1.0
|
O1A
|
A:ADP1102
|
4.5
|
48.0
|
1.0
|
CZ
|
A:ARG822
|
4.7
|
48.5
|
1.0
|
OD2
|
A:ASP443
|
4.9
|
48.5
|
1.0
|
PA
|
A:ADP1102
|
4.9
|
48.0
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 7jl0
Go back to
Fluorine Binding Sites List in 7jl0
Fluorine binding site 2 out
of 4 in the Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)
![](/pictures/F/pdb/jl/7jl0-F-sphere_02.jpg) Mono view
![](/pictures/F/pdb/jl/7jl0-F-sphere_02_stereo.jpg) 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 in Complex with TRIM65 Pspry Domain (Monomer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1103
b:43.8
occ:1.00
|
F2
|
A:ALF1103
|
0.0
|
43.8
|
1.0
|
AL
|
A:ALF1103
|
1.8
|
43.8
|
1.0
|
F3
|
A:ALF1103
|
2.5
|
43.8
|
1.0
|
F4
|
A:ALF1103
|
2.6
|
43.8
|
1.0
|
O2B
|
A:ADP1102
|
2.6
|
48.0
|
1.0
|
O3B
|
A:ADP1102
|
2.9
|
48.0
|
1.0
|
PB
|
A:ADP1102
|
3.0
|
48.0
|
1.0
|
NZ
|
A:LYS335
|
3.2
|
48.5
|
1.0
|
CE
|
A:LYS335
|
3.3
|
48.5
|
1.0
|
F1
|
A:ALF1103
|
3.6
|
43.8
|
1.0
|
O1B
|
A:ADP1102
|
3.6
|
48.0
|
1.0
|
CG2
|
A:THR331
|
3.9
|
48.5
|
1.0
|
CB
|
A:ALA489
|
4.0
|
48.5
|
1.0
|
MG
|
A:MG1104
|
4.2
|
24.6
|
1.0
|
NH2
|
A:ARG822
|
4.2
|
48.5
|
1.0
|
CA
|
A:THR331
|
4.3
|
48.5
|
1.0
|
NE2
|
A:GLN818
|
4.4
|
48.5
|
1.0
|
CB
|
A:THR331
|
4.5
|
48.5
|
1.0
|
O3A
|
A:ADP1102
|
4.5
|
48.0
|
1.0
|
CD
|
A:LYS335
|
4.8
|
48.5
|
1.0
|
O
|
A:THR488
|
5.0
|
48.5
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 7jl0
Go back to
Fluorine Binding Sites List in 7jl0
Fluorine binding site 3 out
of 4 in the Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)
![](/pictures/F/pdb/jl/7jl0-F-sphere_03.jpg) Mono view
![](/pictures/F/pdb/jl/7jl0-F-sphere_03_stereo.jpg) 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 in Complex with TRIM65 Pspry Domain (Monomer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1103
b:43.8
occ:1.00
|
F3
|
A:ALF1103
|
0.0
|
43.8
|
1.0
|
AL
|
A:ALF1103
|
1.8
|
43.8
|
1.0
|
NH2
|
A:ARG822
|
2.2
|
48.5
|
1.0
|
O2B
|
A:ADP1102
|
2.2
|
48.0
|
1.0
|
F2
|
A:ALF1103
|
2.5
|
43.8
|
1.0
|
F1
|
A:ALF1103
|
2.6
|
43.8
|
1.0
|
CZ
|
A:ARG822
|
3.0
|
48.5
|
1.0
|
NH1
|
A:ARG822
|
3.1
|
48.5
|
1.0
|
PB
|
A:ADP1102
|
3.2
|
48.0
|
1.0
|
O1B
|
A:ADP1102
|
3.3
|
48.0
|
1.0
|
F4
|
A:ALF1103
|
3.6
|
43.8
|
1.0
|
NE2
|
A:GLN818
|
3.8
|
48.5
|
1.0
|
O3B
|
A:ADP1102
|
4.1
|
48.0
|
1.0
|
CG2
|
A:THR331
|
4.1
|
48.5
|
1.0
|
NE
|
A:ARG822
|
4.2
|
48.5
|
1.0
|
MG
|
A:MG1104
|
4.4
|
24.6
|
1.0
|
O3A
|
A:ADP1102
|
4.4
|
48.0
|
1.0
|
N
|
A:GLY795
|
4.6
|
42.1
|
1.0
|
CB
|
A:THR331
|
4.6
|
48.5
|
1.0
|
NH2
|
A:ARG824
|
4.7
|
48.5
|
1.0
|
CA
|
A:GLY795
|
4.9
|
42.1
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 7jl0
Go back to
Fluorine Binding Sites List in 7jl0
Fluorine binding site 4 out
of 4 in the Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)
![](/pictures/F/pdb/jl/7jl0-F-sphere_04.jpg) Mono view
![](/pictures/F/pdb/jl/7jl0-F-sphere_04_stereo.jpg) 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 in Complex with TRIM65 Pspry Domain (Monomer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1103
b:43.8
occ:1.00
|
F4
|
A:ALF1103
|
0.0
|
43.8
|
1.0
|
AL
|
A:ALF1103
|
1.8
|
43.8
|
1.0
|
MG
|
A:MG1104
|
1.9
|
24.6
|
1.0
|
F1
|
A:ALF1103
|
2.5
|
43.8
|
1.0
|
F2
|
A:ALF1103
|
2.6
|
43.8
|
1.0
|
O1B
|
A:ADP1102
|
2.6
|
48.0
|
1.0
|
O3B
|
A:ADP1102
|
2.9
|
48.0
|
1.0
|
PB
|
A:ADP1102
|
3.0
|
48.0
|
1.0
|
F3
|
A:ALF1103
|
3.6
|
43.8
|
1.0
|
O2B
|
A:ADP1102
|
3.6
|
48.0
|
1.0
|
CE
|
A:LYS335
|
3.6
|
48.5
|
1.0
|
OD1
|
A:ASP443
|
4.2
|
48.5
|
1.0
|
NZ
|
A:LYS335
|
4.3
|
48.5
|
1.0
|
O3A
|
A:ADP1102
|
4.5
|
48.0
|
1.0
|
CB
|
A:LYS335
|
4.7
|
48.5
|
1.0
|
O2A
|
A:ADP1102
|
4.7
|
48.0
|
1.0
|
OD2
|
A:ASP443
|
4.8
|
48.5
|
1.0
|
CD
|
A:LYS335
|
4.8
|
48.5
|
1.0
|
CG
|
A:ASP443
|
4.9
|
48.5
|
1.0
|
CG
|
A:GLU444
|
4.9
|
48.5
|
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 07:48:59 2024
|