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Fluorine in PDB 6gkh: Cryoem Structure of the MDA5-Dsrna Filament in Complex with Adp-ALF4

Enzymatic activity of Cryoem Structure of the MDA5-Dsrna Filament in Complex with Adp-ALF4

All present enzymatic activity of Cryoem Structure of the MDA5-Dsrna Filament in Complex with Adp-ALF4:
3.6.4.13;

Other elements in 6gkh:

The structure of Cryoem Structure of the MDA5-Dsrna Filament in Complex with Adp-ALF4 also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryoem Structure of the MDA5-Dsrna Filament in Complex with Adp-ALF4 (pdb code 6gkh). 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 the MDA5-Dsrna Filament in Complex with Adp-ALF4, PDB code: 6gkh:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6gkh

Go back to Fluorine Binding Sites List in 6gkh
Fluorine binding site 1 out of 4 in the Cryoem Structure of the MDA5-Dsrna Filament in Complex with Adp-ALF4


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 the MDA5-Dsrna Filament in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:80.4
occ:1.00
F1 A:ALF1102 0.0 80.4 1.0
AL A:ALF1102 1.8 80.4 1.0
MG A:MG1103 2.1 76.5 1.0
O3B A:ADP1101 2.2 84.9 1.0
F3 A:ALF1102 2.5 80.4 1.0
F4 A:ALF1102 2.5 80.4 1.0
O2B A:ADP1101 2.8 84.9 1.0
PB A:ADP1101 2.9 84.9 1.0
HH12 A:ARG822 3.3 76.7 1.0
HA2 A:GLY795 3.5 75.7 1.0
F2 A:ALF1102 3.6 80.4 1.0
H A:GLY795 3.8 75.7 1.0
O3A A:ADP1101 4.0 84.9 1.0
NH1 A:ARG822 4.1 76.7 1.0
O1B A:ADP1101 4.2 84.9 1.0
HH22 A:ARG822 4.2 76.7 1.0
CA A:GLY795 4.3 75.7 1.0
NH2 A:ARG824 4.4 82.4 1.0
N A:GLY795 4.4 75.7 1.0
HH11 A:ARG822 4.4 76.7 1.0
OD1 A:ASP444 4.6 66.0 1.0
O A:GLY795 4.7 75.7 1.0
OE2 A:GLU445 4.8 67.0 1.0
C A:GLY795 4.8 75.7 1.0
O2A A:ADP1101 4.8 84.9 1.0
NH2 A:ARG822 4.8 76.7 1.0
OD2 A:ASP444 4.9 66.0 1.0
CZ A:ARG822 4.9 76.7 1.0

Fluorine binding site 2 out of 4 in 6gkh

Go back to Fluorine Binding Sites List in 6gkh
Fluorine binding site 2 out of 4 in the Cryoem Structure of the MDA5-Dsrna Filament in Complex with Adp-ALF4


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 the MDA5-Dsrna Filament in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:80.4
occ:1.00
F2 A:ALF1102 0.0 80.4 1.0
AL A:ALF1102 1.8 80.4 1.0
O2B A:ADP1101 2.1 84.9 1.0
HZ2 A:LYS336 2.1 74.9 1.0
F4 A:ALF1102 2.5 80.4 1.0
F3 A:ALF1102 2.5 80.4 1.0
HA A:THR332 2.5 77.0 1.0
O1B A:ADP1101 2.6 84.9 1.0
PB A:ADP1101 2.6 84.9 1.0
HG22 A:THR332 2.9 77.0 1.0
HD2 A:LYS336 3.0 74.9 1.0
NZ A:LYS336 3.0 74.9 1.0
HZ3 A:LYS336 3.2 74.9 1.0
H A:GLY333 3.2 79.9 1.0
CA A:THR332 3.4 77.0 1.0
O3B A:ADP1101 3.4 84.9 1.0
HB A:THR332 3.5 77.0 1.0
F1 A:ALF1102 3.6 80.4 1.0
HZ1 A:LYS336 3.6 74.9 1.0
HE3 A:LYS336 3.6 74.9 1.0
CE A:LYS336 3.7 74.9 1.0
CG2 A:THR332 3.7 77.0 1.0
HB2 A:ALA490 3.7 70.4 1.0
CD A:LYS336 3.7 74.9 1.0
CB A:THR332 3.7 77.0 1.0
HE22 A:GLN818 3.8 73.9 1.0
N A:GLY333 3.9 79.9 1.0
O3A A:ADP1101 4.1 84.9 1.0
NH2 A:ARG824 4.1 82.4 1.0
C A:THR332 4.2 77.0 1.0
HD3 A:LYS336 4.3 74.9 1.0
HG21 A:THR332 4.3 77.0 1.0
HG23 A:THR332 4.3 77.0 1.0
HB3 A:ALA490 4.3 70.4 1.0
MG A:MG1103 4.3 76.5 1.0
N A:THR332 4.4 77.0 1.0
CB A:ALA490 4.4 70.4 1.0
HE2 A:LYS336 4.6 74.9 1.0
NE2 A:GLN818 4.6 73.9 1.0
O A:PRO331 4.7 73.1 1.0
HG3 A:LYS336 4.7 74.9 1.0
HB2 A:LYS336 4.7 74.9 1.0
CG A:LYS336 4.8 74.9 1.0
C A:PRO331 4.8 73.1 1.0
H A:THR332 4.9 77.0 1.0
OE2 A:GLU445 4.9 67.0 1.0
HH12 A:ARG822 5.0 76.7 1.0

Fluorine binding site 3 out of 4 in 6gkh

Go back to Fluorine Binding Sites List in 6gkh
Fluorine binding site 3 out of 4 in the Cryoem Structure of the MDA5-Dsrna Filament in Complex with Adp-ALF4


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 the MDA5-Dsrna Filament in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:80.4
occ:1.00
F3 A:ALF1102 0.0 80.4 1.0
O2B A:ADP1101 1.6 84.9 1.0
AL A:ALF1102 1.8 80.4 1.0
HH12 A:ARG822 2.5 76.7 1.0
F2 A:ALF1102 2.5 80.4 1.0
F1 A:ALF1102 2.5 80.4 1.0
NH2 A:ARG824 2.7 82.4 1.0
NH1 A:ARG822 2.9 76.7 1.0
PB A:ADP1101 3.0 84.9 1.0
HB A:THR332 3.2 77.0 1.0
HH11 A:ARG822 3.2 76.7 1.0
HG22 A:THR332 3.4 77.0 1.0
HH22 A:ARG822 3.4 76.7 1.0
O3B A:ADP1101 3.5 84.9 1.0
CZ A:ARG822 3.6 76.7 1.0
F4 A:ALF1102 3.6 80.4 1.0
NH2 A:ARG822 3.7 76.7 1.0
HE22 A:GLN818 3.9 73.9 1.0
CB A:THR332 3.9 77.0 1.0
CG2 A:THR332 4.0 77.0 1.0
O3A A:ADP1101 4.0 84.9 1.0
CZ A:ARG824 4.0 82.4 1.0
HA A:THR332 4.0 77.0 1.0
HG21 A:THR332 4.0 77.0 1.0
H A:GLY333 4.0 79.9 1.0
O1B A:ADP1101 4.0 84.9 1.0
H A:GLY795 4.2 75.7 1.0
MG A:MG1103 4.3 76.5 1.0
HH21 A:ARG822 4.4 76.7 1.0
NE2 A:GLN818 4.4 73.9 1.0
CA A:THR332 4.5 77.0 1.0
HE21 A:GLN818 4.5 73.9 1.0
HD3 A:ARG822 4.5 76.7 1.0
NE A:ARG822 4.6 76.7 1.0
HZ2 A:LYS336 4.6 74.9 1.0
N A:GLY333 4.6 79.9 1.0
NH1 A:ARG824 4.6 82.4 1.0
O A:GLY795 4.7 75.7 1.0
NE A:ARG824 4.8 82.4 1.0
HG23 A:THR332 4.9 77.0 1.0
HA2 A:GLY795 4.9 75.7 1.0
N A:GLY795 5.0 75.7 1.0

Fluorine binding site 4 out of 4 in 6gkh

Go back to Fluorine Binding Sites List in 6gkh
Fluorine binding site 4 out of 4 in the Cryoem Structure of the MDA5-Dsrna Filament in Complex with Adp-ALF4


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 the MDA5-Dsrna Filament in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:80.4
occ:1.00
F4 A:ALF1102 0.0 80.4 1.0
AL A:ALF1102 1.8 80.4 1.0
MG A:MG1103 2.1 76.5 1.0
O3B A:ADP1101 2.1 84.9 1.0
F2 A:ALF1102 2.5 80.4 1.0
F1 A:ALF1102 2.5 80.4 1.0
PB A:ADP1101 2.6 84.9 1.0
HD2 A:LYS336 2.6 74.9 1.0
O1B A:ADP1101 2.8 84.9 1.0
O2B A:ADP1101 3.1 84.9 1.0
CD A:LYS336 3.5 74.9 1.0
F3 A:ALF1102 3.6 80.4 1.0
HB2 A:LYS336 3.6 74.9 1.0
HZ2 A:LYS336 3.6 74.9 1.0
OD1 A:ASP444 3.7 66.0 1.0
HD3 A:LYS336 3.7 74.9 1.0
HZ3 A:LYS336 3.8 74.9 1.0
NZ A:LYS336 4.1 74.9 1.0
O3A A:ADP1101 4.1 84.9 1.0
HB3 A:LYS336 4.2 74.9 1.0
CB A:LYS336 4.2 74.9 1.0
CE A:LYS336 4.4 74.9 1.0
CG A:LYS336 4.4 74.9 1.0
OE2 A:GLU445 4.6 67.0 1.0
O1A A:ADP1101 4.6 84.9 1.0
HE3 A:LYS336 4.7 74.9 1.0
HG3 A:LYS336 4.7 74.9 1.0
CG A:ASP444 4.7 66.0 1.0
H A:GLY333 4.7 79.9 1.0
PA A:ADP1101 4.8 84.9 1.0
HA A:THR332 4.9 77.0 1.0
HZ1 A:LYS336 4.9 74.9 1.0
OD2 A:ASP444 4.9 66.0 1.0

Reference:

Q.Yu, K.Qu, Y.Modis. Cryo-Em Structures of MDA5-Dsrna Filaments at Different Stages of Atp Hydrolysis. Mol. Cell V. 72 999 2018.
ISSN: ISSN 1097-4164
PubMed: 30449722
DOI: 10.1016/J.MOLCEL.2018.10.012
Page generated: Thu Aug 1 20:34:04 2024

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