Fluorine in PDB 7n72: Cryo-Em Structure of ATP13A2 in the Alf-Bound E2-Pi-Like State

The structure of Cryo-Em Structure of ATP13A2 in the Alf-Bound E2-Pi-Like State also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Cryo-Em Structure of ATP13A2 in the Alf-Bound E2-Pi-Like State (pdb code 7n72). 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 ATP13A2 in the Alf-Bound E2-Pi-Like State, PDB code: 7n72:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cryo-Em Structure of ATP13A2 in the Alf-Bound E2-Pi-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 Alf-Bound E2-Pi-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:42.4 occ:1.00 F1 A:ALF1201 0.0 42.4 1.0 AL A:ALF1201 1.7 42.4 1.0 OG1 A:THR745 2.4 38.2 1.0 F4 A:ALF1201 2.4 42.4 1.0 OD1 A:ASP508 2.4 39.9 1.0 N A:GLY746 2.4 39.5 1.0 F3 A:ALF1201 2.5 42.4 1.0 CA A:THR745 2.7 38.2 1.0 C A:THR745 3.0 38.2 1.0 CB A:THR745 3.0 38.2 1.0 NZ A:LYS854 3.5 42.6 1.0 F2 A:ALF1201 3.5 42.4 1.0 CA A:GLY746 3.6 39.5 1.0 CG A:ASP508 3.7 39.9 1.0 O A:THR341 3.8 41.7 1.0 N A:THR745 4.0 38.2 1.0 O A:VAL744 4.0 38.0 1.0 N A:LYS509 4.1 37.6 1.0 N A:ASP747 4.1 40.7 1.0 CE A:LYS854 4.2 42.6 1.0 ND2 A:ASN876 4.2 43.3 1.0 O A:THR745 4.2 38.2 1.0 CG2 A:THR745 4.3 38.2 1.0 C A:GLY746 4.4 39.5 1.0 OE2 A:GLU343 4.4 42.2 1.0 C A:VAL744 4.5 38.0 1.0 OD2 A:ASP508 4.5 39.9 1.0 CB A:ASP508 4.5 39.9 1.0 CA A:ASP508 4.6 39.9 1.0 CB A:LYS509 4.8 37.6 1.0 N A:THR510 4.9 40.3 1.0 C A:ASP508 4.9 39.9 1.0 C A:THR341 5.0 41.7 1.0 CA A:LYS509 5.0 37.6 1.0

Fluorine binding site 2 out of 4 in the Cryo-Em Structure of ATP13A2 in the Alf-Bound E2-Pi-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 Alf-Bound E2-Pi-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:42.4 occ:1.00 F2 A:ALF1201 0.0 42.4 1.0 AL A:ALF1201 1.8 42.4 1.0 MG A:MG1202 2.0 42.5 1.0 OD2 A:ASP508 2.4 39.9 1.0 OD1 A:ASP508 2.4 39.9 1.0 F3 A:ALF1201 2.5 42.4 1.0 F4 A:ALF1201 2.6 42.4 1.0 CG A:ASP508 2.7 39.9 1.0 O A:THR510 2.9 40.3 1.0 CB A:THR510 3.5 40.3 1.0 N A:THR510 3.5 40.3 1.0 F1 A:ALF1201 3.5 42.4 1.0 C A:THR510 3.7 40.3 1.0 CA A:THR510 3.7 40.3 1.0 O A:GLY342 3.8 40.7 1.0 CA A:GLY342 4.0 40.7 1.0 OG1 A:THR510 4.1 40.3 1.0 OD1 A:ASP873 4.1 42.9 1.0 C A:GLY342 4.2 40.7 1.0 CB A:ASP508 4.2 39.9 1.0 OE2 A:GLU343 4.3 42.2 1.0 N A:LYS509 4.5 37.6 1.0 C A:LYS509 4.5 37.6 1.0 CG2 A:THR510 4.6 40.3 1.0 O A:THR341 4.7 41.7 1.0 OD2 A:ASP877 4.7 44.0 1.0 ND2 A:ASN876 4.9 43.3 1.0 N A:GLY511 4.9 41.8 1.0 OD1 A:ASN876 4.9 43.3 1.0 OG1 A:THR745 5.0 38.2 1.0 C A:ASP508 5.0 39.9 1.0

Fluorine binding site 3 out of 4 in the Cryo-Em Structure of ATP13A2 in the Alf-Bound E2-Pi-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 Alf-Bound E2-Pi-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:42.4 occ:1.00 F3 A:ALF1201 0.0 42.4 1.0 AL A:ALF1201 1.8 42.4 1.0 F2 A:ALF1201 2.5 42.4 1.0 F1 A:ALF1201 2.5 42.4 1.0 OD1 A:ASP508 2.5 39.9 1.0 ND2 A:ASN876 2.5 43.3 1.0 O A:THR341 3.2 41.7 1.0 CG A:ASP508 3.2 39.9 1.0 CG A:ASN876 3.4 43.3 1.0 NZ A:LYS854 3.4 42.6 1.0 OD1 A:ASN876 3.4 43.3 1.0 F4 A:ALF1201 3.5 42.4 1.0 CA A:GLY342 3.5 40.7 1.0 OD2 A:ASP508 3.5 39.9 1.0 MG A:MG1202 3.8 42.5 1.0 C A:THR341 3.9 41.7 1.0 OD2 A:ASP877 4.0 44.0 1.0 N A:GLY342 4.0 40.7 1.0 N A:GLY746 4.2 39.5 1.0 OD1 A:ASP877 4.2 44.0 1.0 CB A:ASP508 4.4 39.9 1.0 CE A:LYS854 4.4 42.6 1.0 C A:GLY342 4.5 40.7 1.0 CG A:ASP877 4.5 44.0 1.0 O A:GLY342 4.7 40.7 1.0 OG1 A:THR745 4.7 38.2 1.0 CB A:ASN876 4.8 43.3 1.0 CA A:GLY746 4.9 39.5 1.0 OE2 A:GLU343 4.9 42.2 1.0 CA A:THR745 5.0 38.2 1.0

Fluorine binding site 4 out of 4 in the Cryo-Em Structure of ATP13A2 in the Alf-Bound E2-Pi-Like 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 ATP13A2 in the Alf-Bound E2-Pi-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:42.4 occ:1.00 F4 A:ALF1201 0.0 42.4 1.0 AL A:ALF1201 1.8 42.4 1.0 F1 A:ALF1201 2.4 42.4 1.0 OD1 A:ASP508 2.4 39.9 1.0 N A:THR510 2.5 40.3 1.0 OG1 A:THR745 2.6 38.2 1.0 F2 A:ALF1201 2.6 42.4 1.0 N A:LYS509 3.0 37.6 1.0 CB A:LYS509 3.2 37.6 1.0 OG1 A:THR510 3.2 40.3 1.0 CA A:LYS509 3.3 37.6 1.0 C A:LYS509 3.3 37.6 1.0 CG A:ASP508 3.4 39.9 1.0 CB A:THR510 3.5 40.3 1.0 F3 A:ALF1201 3.5 42.4 1.0 CA A:THR510 3.5 40.3 1.0 OE2 A:GLU343 3.5 42.2 1.0 CB A:THR745 3.6 38.2 1.0 OD2 A:ASP508 3.8 39.9 1.0 C A:ASP508 4.1 39.9 1.0 O A:THR510 4.1 40.3 1.0 CA A:THR745 4.2 38.2 1.0 C A:THR510 4.3 40.3 1.0 CE A:LYS509 4.4 37.6 1.0 CG A:LYS509 4.4 37.6 1.0 MG A:MG1202 4.4 42.5 1.0 NZ A:LYS509 4.4 37.6 1.0 N A:GLY746 4.5 39.5 1.0 CB A:ASP508 4.5 39.9 1.0 O A:LYS509 4.5 37.6 1.0 CA A:ASP508 4.5 39.9 1.0 CD A:GLU343 4.7 42.2 1.0 CG2 A:THR745 4.9 38.2 1.0 C A:THR745 4.9 38.2 1.0 CD A:LYS509 5.0 37.6 1.0 CG2 A:THR510 5.0 40.3 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