Fluorine in PDB 6gkh: 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;

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

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 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 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 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 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

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