Fluorine in PDB 6k7m: Cryo-Em Structure of the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State)

All present enzymatic activity of Cryo-Em Structure of the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State):
7.6.2.1;

The structure of Cryo-Em Structure of the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State) also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Cryo-Em Structure of the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State) (pdb code 6k7m). 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 the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State), PDB code: 6k7m:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cryo-Em Structure of the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State)


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 the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1301 b:45.6 occ:1.00 F1 A:ALF1301 0.0 45.6 1.0 AL A:ALF1301 1.8 45.6 1.0 N A:GLY671 2.4 55.6 1.0 F4 A:ALF1301 2.5 45.6 1.0 F3 A:ALF1301 2.5 45.6 1.0 NZ A:LYS766 3.0 47.4 1.0 C A:THR670 3.2 50.7 1.0 CA A:THR670 3.2 50.7 1.0 CA A:GLY671 3.3 55.6 1.0 CE A:LYS766 3.5 47.4 1.0 F2 A:ALF1301 3.6 45.6 1.0 O A:LEU669 3.7 43.9 1.0 CB A:ASP409 3.9 41.0 1.0 OG1 A:THR670 4.0 50.7 1.0 O A:ASP189 4.0 62.7 1.0 ND2 A:ASN789 4.1 46.5 1.0 CB A:THR670 4.1 50.7 1.0 OD2 A:ASP409 4.2 41.0 1.0 N A:THR670 4.2 50.7 1.0 O A:THR670 4.3 50.7 1.0 C A:GLY671 4.4 55.6 1.0 C A:LEU669 4.4 43.9 1.0 CG A:ASP409 4.6 41.0 1.0 N A:ASP672 4.6 62.1 1.0 OD1 A:ASP790 4.8 41.2 1.0 N A:LYS410 4.8 46.5 1.0 CA A:ASP409 4.8 41.0 1.0 OE2 A:GLU191 4.9 65.7 1.0 C A:ASP189 4.9 62.7 1.0 CD A:LYS766 5.0 47.4 1.0

Fluorine binding site 2 out of 4 in the Cryo-Em Structure of the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State)


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 the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1301 b:45.6 occ:1.00 F2 A:ALF1301 0.0 45.6 1.0 AL A:ALF1301 1.8 45.6 1.0 MG A:MG1303 2.0 44.4 1.0 OD2 A:ASP409 2.3 41.0 1.0 F3 A:ALF1301 2.5 45.6 1.0 F4 A:ALF1301 2.6 45.6 1.0 O A:THR411 2.9 46.7 1.0 CG A:ASP409 3.4 41.0 1.0 F1 A:ALF1301 3.6 45.6 1.0 N A:THR411 3.7 46.7 1.0 OD1 A:ASP786 3.7 39.9 1.0 CB A:THR411 3.8 46.7 1.0 C A:THR411 3.8 46.7 1.0 O A:GLY190 3.9 62.6 1.0 CA A:GLY190 3.9 62.6 1.0 CA A:THR411 4.0 46.7 1.0 CB A:ASP409 4.1 41.0 1.0 OE2 A:GLU191 4.2 65.7 1.0 C A:GLY190 4.2 62.6 1.0 OD2 A:ASP790 4.3 41.2 1.0 OD1 A:ASP409 4.4 41.0 1.0 N A:LYS410 4.4 46.5 1.0 OD1 A:ASN789 4.5 46.5 1.0 CG2 A:THR411 4.6 46.7 1.0 C A:LYS410 4.7 46.5 1.0 OG1 A:THR411 4.7 46.7 1.0 O A:ASP189 4.8 62.7 1.0 CG A:ASP786 4.9 39.9 1.0

Fluorine binding site 3 out of 4 in the Cryo-Em Structure of the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State)


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 the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1301 b:45.6 occ:1.00 F3 A:ALF1301 0.0 45.6 1.0 AL A:ALF1301 1.8 45.6 1.0 F2 A:ALF1301 2.5 45.6 1.0 F1 A:ALF1301 2.5 45.6 1.0 ND2 A:ASN789 2.7 46.5 1.0 OD1 A:ASN789 2.8 46.5 1.0 NZ A:LYS766 3.1 47.4 1.0 CG A:ASN789 3.1 46.5 1.0 OD2 A:ASP409 3.2 41.0 1.0 OD2 A:ASP790 3.4 41.2 1.0 MG A:MG1303 3.6 44.4 1.0 F4 A:ALF1301 3.6 45.6 1.0 OD1 A:ASP790 3.6 41.2 1.0 CA A:GLY190 3.6 62.6 1.0 O A:ASP189 3.8 62.7 1.0 CG A:ASP790 3.9 41.2 1.0 CG A:ASP409 4.0 41.0 1.0 CB A:ASP409 4.1 41.0 1.0 N A:GLY190 4.2 62.6 1.0 C A:ASP189 4.3 62.7 1.0 CE A:LYS766 4.3 47.4 1.0 CB A:ASN789 4.6 46.5 1.0 N A:GLY671 4.7 55.6 1.0 C A:GLY190 4.7 62.6 1.0

Fluorine binding site 4 out of 4 in the Cryo-Em Structure of the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State)


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 the Human P4-Type Flippase ATP8A1-CDC50 (E2PI-Pl State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1301 b:45.6 occ:1.00 F4 A:ALF1301 0.0 45.6 1.0 AL A:ALF1301 1.8 45.6 1.0 F1 A:ALF1301 2.5 45.6 1.0 F2 A:ALF1301 2.6 45.6 1.0 N A:THR411 3.2 46.7 1.0 N A:LYS410 3.3 46.5 1.0 OG1 A:THR670 3.3 50.7 1.0 F3 A:ALF1301 3.6 45.6 1.0 OD2 A:ASP409 3.6 41.0 1.0 OE2 A:GLU191 3.6 65.7 1.0 N A:GLY671 3.8 55.6 1.0 CB A:LYS410 3.8 46.5 1.0 CA A:LYS410 3.9 46.5 1.0 CB A:THR411 3.9 46.7 1.0 CB A:THR670 3.9 50.7 1.0 CA A:THR670 3.9 50.7 1.0 C A:LYS410 4.0 46.5 1.0 CB A:ASP409 4.0 41.0 1.0 CA A:THR411 4.1 46.7 1.0 OG1 A:THR411 4.1 46.7 1.0 CG A:ASP409 4.1 41.0 1.0 C A:ASP409 4.3 41.0 1.0 C A:THR670 4.4 50.7 1.0 O A:THR411 4.4 46.7 1.0 CA A:ASP409 4.5 41.0 1.0 MG A:MG1303 4.5 44.4 1.0 N A:ASP672 4.7 62.1 1.0 CA A:GLY671 4.7 55.6 1.0 C A:THR411 4.7 46.7 1.0 CD A:GLU191 4.8 65.7 1.0 O A:ASP189 4.9 62.7 1.0 O A:LEU669 4.9 43.9 1.0 CE A:LYS410 4.9 46.5 1.0

M.Hiraizumi, K.Yamashita, T.Nishizawa, O.Nureki. Cryo-Em Structures Capture the Transport Cycle of the P4-Atpase Flippase. Science V. 365 1149 2019.
ISSN: ESSN 1095-9203
PubMed: 31416931
DOI: 10.1126/SCIENCE.AAY3353