Fluorine in PDB 7nic: Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class)

Enzymatic activity of Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class)

All present enzymatic activity of Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class):
3.6.4.13;

Other elements in 7nic:

The structure of Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class) also contains other interesting chemical elements:

Aluminium (Al) 1 atom
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class) (pdb code 7nic). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class), PDB code: 7nic:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7nic

Go back to Fluorine Binding Sites List in 7nic
Fluorine binding site 1 out of 4 in the Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:113.6
occ:1.00
 F1 A:ALF1102 0.0 113.6 1.0
AL A:ALF1102 1.8 113.6 1.0
F4 A:ALF1102 2.5 113.6 1.0
F3 A:ALF1102 2.5 113.6 1.0
O3B A:ADP1101 2.8 111.5 1.0
HA2 A:GLY795 3.1 105.5 1.0
H A:GLY795 3.3 105.5 1.0
O2B A:ADP1101 3.4 111.5 1.0
F2 A:ALF1102 3.6 113.6 1.0
PB A:ADP1101 3.6 111.5 1.0
OE2 A:GLU445 3.7 95.1 1.0
CA A:GLY795 3.9 105.5 1.0
N A:GLY795 4.0 105.5 1.0
O3A A:ADP1101 4.4 111.5 1.0
HA3 A:GLY795 4.6 105.5 1.0
HD11 A:LEU369 4.6 97.8 1.0
HD23 A:LEU369 4.7 97.8 1.0
C A:GLY795 4.8 105.5 1.0
OD2 A:ASP444 4.8 90.9 1.0
CD A:GLU445 4.8 95.1 1.0
O A:GLY795 4.8 105.5 1.0
HD2 A:LYS336 4.9 105.8 1.0
O1B A:ADP1101 5.0 111.5 1.0
HH12 A:ARG822 5.0 111.5 1.0
H A:GLY333 5.0 112.8 1.0

Fluorine binding site 2 out of 4 in 7nic

Go back to Fluorine Binding Sites List in 7nic
Fluorine binding site 2 out of 4 in the Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:113.6
occ:1.00
 F2 A:ALF1102 0.0 113.6 1.0
HZ3 A:LYS336 1.7 105.8 1.0
AL A:ALF1102 1.8 113.6 1.0
O2B A:ADP1101 2.3 111.5 1.0
HA A:THR332 2.4 110.2 1.0
F3 A:ALF1102 2.5 113.6 1.0
F4 A:ALF1102 2.5 113.6 1.0
NZ A:LYS336 2.5 105.8 1.0
HD2 A:LYS336 2.6 105.8 1.0
PB A:ADP1101 2.9 111.5 1.0
HZ1 A:LYS336 2.9 105.8 1.0
HG22 A:THR332 3.0 110.2 1.0
HZ2 A:LYS336 3.1 105.8 1.0
O3B A:ADP1101 3.2 111.5 1.0
CE A:LYS336 3.2 105.8 1.0
O1B A:ADP1101 3.3 111.5 1.0
HE3 A:LYS336 3.3 105.8 1.0
HB3 A:ALA490 3.3 107.7 1.0
CD A:LYS336 3.4 105.8 1.0
CA A:THR332 3.4 110.2 1.0
H A:GLY333 3.5 112.8 1.0
F1 A:ALF1102 3.6 113.6 1.0
CG2 A:THR332 3.8 110.2 1.0
HB A:THR332 3.8 110.2 1.0
HD3 A:LYS336 3.8 105.8 1.0
CB A:THR332 3.9 110.2 1.0
HB2 A:ALA490 4.0 107.7 1.0
HE22 A:GLN818 4.1 113.0 1.0
N A:GLY333 4.1 112.8 1.0
CB A:ALA490 4.1 107.7 1.0
HE2 A:LYS336 4.2 105.8 1.0
N A:THR332 4.2 110.2 1.0
HG23 A:THR332 4.2 110.2 1.0
C A:THR332 4.3 110.2 1.0
O A:PRO331 4.3 104.7 1.0
O3A A:ADP1101 4.4 111.5 1.0
OE1 A:GLN818 4.5 113.0 1.0
HG21 A:THR332 4.5 110.2 1.0
C A:PRO331 4.5 104.7 1.0
HG3 A:LYS336 4.5 105.8 1.0
CG A:LYS336 4.5 105.8 1.0
HB2 A:LYS336 4.7 105.8 1.0
H A:THR332 4.7 110.2 1.0
HB1 A:ALA490 4.8 107.7 1.0
O A:LEU330 4.8 105.7 1.0
NE2 A:GLN818 4.8 113.0 1.0
N A:ALA490 5.0 107.7 1.0
CA A:ALA490 5.0 107.7 1.0
HA A:ALA490 5.0 107.7 1.0

Fluorine binding site 3 out of 4 in 7nic

Go back to Fluorine Binding Sites List in 7nic
Fluorine binding site 3 out of 4 in the Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:113.6
occ:1.00
 F3 A:ALF1102 0.0 113.6 1.0
AL A:ALF1102 1.8 113.6 1.0
O2B A:ADP1101 2.3 111.5 1.0
F2 A:ALF1102 2.5 113.6 1.0
F1 A:ALF1102 2.5 113.6 1.0
HG22 A:THR332 2.8 110.2 1.0
HB A:THR332 3.0 110.2 1.0
HA A:THR332 3.4 110.2 1.0
CG2 A:THR332 3.5 110.2 1.0
OE1 A:GLN818 3.5 113.0 1.0
H A:GLY333 3.5 112.8 1.0
PB A:ADP1101 3.5 111.5 1.0
CB A:THR332 3.6 110.2 1.0
F4 A:ALF1102 3.6 113.6 1.0
HH21 A:ARG824 3.6 119.7 1.0
HG21 A:THR332 3.6 110.2 1.0
O3B A:ADP1101 3.7 111.5 1.0
CA A:THR332 4.0 110.2 1.0
HZ3 A:LYS336 4.1 105.8 1.0
NH2 A:ARG824 4.2 119.7 1.0
HH22 A:ARG824 4.2 119.7 1.0
N A:GLY333 4.3 112.8 1.0
HG23 A:THR332 4.3 110.2 1.0
HE22 A:GLN818 4.4 113.0 1.0
H A:GLY795 4.4 105.5 1.0
O3A A:ADP1101 4.4 111.5 1.0
CD A:GLN818 4.5 113.0 1.0
HH12 A:ARG822 4.6 111.5 1.0
O1B A:ADP1101 4.6 111.5 1.0
HH11 A:ARG822 4.7 111.5 1.0
C A:THR332 4.7 110.2 1.0
HB3 A:ALA490 4.8 107.7 1.0
HA2 A:GLY795 4.8 105.5 1.0
HD2 A:LYS336 4.9 105.8 1.0
OG1 A:THR332 4.9 110.2 1.0
NE2 A:GLN818 4.9 113.0 1.0
NH1 A:ARG822 5.0 111.5 1.0
NZ A:LYS336 5.0 105.8 1.0
HG1 A:THR332 5.0 110.2 1.0

Fluorine binding site 4 out of 4 in 7nic

Go back to Fluorine Binding Sites List in 7nic
Fluorine binding site 4 out of 4 in the Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryoem Structure of Disease Related M854K MDA5-Dsrna Filament in Complex with Adp-ALF4(Minor Class) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:113.6
occ:1.00
 F4 A:ALF1102 0.0 113.6 1.0
AL A:ALF1102 1.8 113.6 1.0
O3B A:ADP1101 2.1 111.5 1.0
F1 A:ALF1102 2.5 113.6 1.0
F2 A:ALF1102 2.5 113.6 1.0
HD2 A:LYS336 2.6 105.8 1.0
PB A:ADP1101 3.0 111.5 1.0
O2B A:ADP1101 3.4 111.5 1.0
HZ3 A:LYS336 3.5 105.8 1.0
CD A:LYS336 3.5 105.8 1.0
F3 A:ALF1102 3.6 113.6 1.0
HD3 A:LYS336 3.6 105.8 1.0
O1B A:ADP1101 3.7 111.5 1.0
OE2 A:GLU445 3.7 95.1 1.0
HB2 A:LYS336 3.7 105.8 1.0
HZ1 A:LYS336 3.9 105.8 1.0
NZ A:LYS336 4.0 105.8 1.0
OD1 A:ASP444 4.1 90.9 1.0
CE A:LYS336 4.3 105.8 1.0
CB A:LYS336 4.4 105.8 1.0
HB3 A:LYS336 4.4 105.8 1.0
O3A A:ADP1101 4.4 111.5 1.0
OD2 A:ASP444 4.4 90.9 1.0
CG A:LYS336 4.5 105.8 1.0
CG A:ASP444 4.7 90.9 1.0
HE3 A:LYS336 4.7 105.8 1.0
HG3 A:LYS336 4.8 105.8 1.0
HA A:THR332 4.8 110.2 1.0
HZ2 A:LYS336 4.8 105.8 1.0
CD A:GLU445 4.9 95.1 1.0
HA A:THR489 4.9 98.9 1.0
H A:GLY333 5.0 112.8 1.0
HB3 A:ALA490 5.0 107.7 1.0

Reference:

Q.Yu, A.Herrero Del Valle, R.Singh, Y.Modis. MDA5 Autoimmune Disease Variant M854K Prevents Atp-Dependent Structural Discrimination of Viral and Cellular Rna. Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-27062-5
Page generated: Fri Aug 2 10:05:39 2024

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