Fluorine in PDB 7n70: Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State

The structure of Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State (pdb code 7n70). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State, PDB code: 7n70:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like 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 ATP13A2 in the Bef-Bound E2P-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:32.4 occ:1.00 F1 A:BEF1201 0.0 32.4 1.0 BE A:BEF1201 1.5 32.4 1.0 OD2 A:ASP508 2.1 31.7 1.0 MG A:MG1202 2.2 30.8 1.0 OD1 A:ASP508 2.4 31.7 1.0 F3 A:BEF1201 2.5 32.4 1.0 F2 A:BEF1201 2.6 32.4 1.0 CG A:ASP508 2.6 31.7 1.0 O A:THR510 3.0 30.4 1.0 CA A:GLY342 3.7 31.8 1.0 N A:THR510 3.8 30.4 1.0 ND2 A:ASN876 3.8 34.4 1.0 CB A:THR510 3.9 30.4 1.0 C A:THR510 3.9 30.4 1.0 O A:SER338 4.0 32.3 1.0 CA A:THR510 4.0 30.4 1.0 CB A:ASP508 4.1 31.7 1.0 OD1 A:ASP873 4.2 36.1 1.0 OD2 A:ASP877 4.2 36.6 1.0 OD1 A:ASN876 4.4 34.4 1.0 OG1 A:THR510 4.4 30.4 1.0 NZ A:LYS854 4.5 30.2 1.0 N A:LYS509 4.5 28.6 1.0 O A:GLY342 4.5 31.8 1.0 CG A:ASN876 4.5 34.4 1.0 N A:GLY342 4.6 31.8 1.0 C A:GLY342 4.6 31.8 1.0 C A:LYS509 4.8 28.6 1.0 CA A:ASP508 5.0 31.7 1.0 OG1 A:THR745 5.0 28.8 1.0

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like 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 ATP13A2 in the Bef-Bound E2P-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:32.4 occ:1.00 F2 A:BEF1201 0.0 32.4 1.0 BE A:BEF1201 1.6 32.4 1.0 OG1 A:THR745 2.4 28.8 1.0 OD1 A:ASP508 2.4 31.7 1.0 F3 A:BEF1201 2.5 32.4 1.0 F1 A:BEF1201 2.6 32.4 1.0 N A:THR510 3.2 30.4 1.0 CB A:THR745 3.3 28.8 1.0 OG1 A:THR510 3.4 30.4 1.0 N A:GLY746 3.4 28.4 1.0 CG A:ASP508 3.5 31.7 1.0 CA A:THR745 3.5 28.8 1.0 O A:GLY342 3.6 31.8 1.0 N A:LYS509 3.6 28.6 1.0 CB A:THR510 3.7 30.4 1.0 CA A:GLY342 3.7 31.8 1.0 OD2 A:ASP508 3.9 31.7 1.0 C A:THR745 4.0 28.8 1.0 CA A:THR510 4.0 30.4 1.0 CB A:LYS509 4.0 28.6 1.0 CA A:LYS509 4.1 28.6 1.0 C A:LYS509 4.1 28.6 1.0 C A:GLY342 4.1 31.8 1.0 N A:ASP747 4.4 30.7 1.0 O A:THR510 4.4 30.4 1.0 CA A:GLY746 4.5 28.4 1.0 NZ A:LYS854 4.5 30.2 1.0 MG A:MG1202 4.6 30.8 1.0 C A:ASP508 4.6 31.7 1.0 CG2 A:THR745 4.7 28.8 1.0 CB A:ASP508 4.7 31.7 1.0 C A:THR510 4.7 30.4 1.0 O A:VAL744 4.8 28.6 1.0 ND2 A:ASN876 4.8 34.4 1.0 CA A:ASP508 4.8 31.7 1.0 N A:THR745 4.8 28.8 1.0 C A:GLY746 4.9 28.4 1.0 CE A:LYS509 4.9 28.6 1.0 CB A:ASP747 5.0 30.7 1.0

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like 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 ATP13A2 in the Bef-Bound E2P-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:32.4 occ:1.00 F3 A:BEF1201 0.0 32.4 1.0 BE A:BEF1201 1.5 32.4 1.0 OD1 A:ASP508 2.3 31.7 1.0 NZ A:LYS854 2.4 30.2 1.0 F2 A:BEF1201 2.5 32.4 1.0 ND2 A:ASN876 2.5 34.4 1.0 F1 A:BEF1201 2.5 32.4 1.0 CG A:ASP508 3.2 31.7 1.0 N A:GLY746 3.3 28.4 1.0 CE A:LYS854 3.4 30.2 1.0 OD2 A:ASP508 3.6 31.7 1.0 CG A:ASN876 3.7 34.4 1.0 CA A:THR745 3.8 28.8 1.0 CA A:GLY342 3.8 31.8 1.0 C A:THR745 3.9 28.8 1.0 OD1 A:ASP877 4.0 36.6 1.0 CA A:GLY746 4.1 28.4 1.0 OG1 A:THR745 4.1 28.8 1.0 OD1 A:ASN876 4.3 34.4 1.0 O A:VAL744 4.3 28.6 1.0 CB A:ASP508 4.4 31.7 1.0 OD2 A:ASP877 4.5 36.6 1.0 MG A:MG1202 4.5 30.8 1.0 N A:GLY342 4.5 31.8 1.0 CB A:THR745 4.6 28.8 1.0 CG A:ASP877 4.7 36.6 1.0 O A:THR341 4.7 32.6 1.0 CD A:LYS854 4.7 30.2 1.0 N A:THR745 4.9 28.8 1.0 CB A:ASN876 4.9 34.4 1.0 C A:GLY342 4.9 31.8 1.0 C A:THR341 4.9 32.6 1.0 N A:LYS509 4.9 28.6 1.0 CA A:ASP508 5.0 31.7 1.0 O A:GLY342 5.0 31.8 1.0 O A:THR745 5.0 28.8 1.0

S.I.Sim, S.Von Bulow, G.Hummer, E.Park. Structural Basis of Polyamine Transport By Human ATP13A2 (PARK9). Mol.Cell 2021.
ISSN: ISSN 1097-2765
PubMed: 34715013
DOI: 10.1016/J.MOLCEL.2021.08.017