Fluorine in PDB 8ieo: Cryo-Em Structure of ATP13A2 in the Nominal E1P State

The structure of Cryo-Em Structure of ATP13A2 in the Nominal E1P 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 Nominal E1P State (pdb code 8ieo). 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 Nominal E1P State, PDB code: 8ieo:
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 Nominal E1P 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 Nominal E1P State within 5.0Å range: probe atom residue distance (Å) B Occ P:F1201 b:3.6 occ:1.00 F1 P:ALF1201 0.0 3.6 1.0 AL P:ALF1201 1.8 3.6 1.0 MG P:MG1202 2.1 16.3 1.0 F4 P:ALF1201 2.5 3.6 1.0 F3 P:ALF1201 2.5 3.6 1.0 O P:THR515 2.6 5.4 1.0 HB P:THR515 2.8 5.4 1.0 OD2 P:ASP513 3.1 3.7 1.0 HB2 P:ASP513 3.2 3.7 1.0 C P:THR515 3.3 5.4 1.0 OD1 P:ASP878 3.3 8.6 1.0 F2 P:ALF1201 3.6 3.6 1.0 CB P:THR515 3.7 5.4 1.0 HA3 P:GLY516 3.7 4.9 1.0 CG P:ASP513 3.7 3.7 1.0 H P:THR515 3.8 5.4 1.0 CA P:THR515 3.9 5.4 1.0 CB P:ASP513 3.9 3.7 1.0 HA3 P:GLY347 4.1 8.9 1.0 N P:GLY516 4.1 4.9 1.0 HG22 P:THR515 4.1 5.4 1.0 HA2 P:GLY347 4.2 8.9 1.0 N P:THR515 4.2 5.4 1.0 HB3 P:ASP513 4.3 3.7 1.0 CA P:GLY516 4.4 4.9 1.0 CG2 P:THR515 4.4 5.4 1.0 H P:ASP878 4.5 8.6 1.0 CG P:ASP878 4.5 8.6 1.0 CA P:GLY347 4.6 8.9 1.0 H P:GLY879 4.6 11.4 1.0 OG1 P:THR515 4.7 5.4 1.0 OD1 P:ASP513 4.7 3.7 1.0 HG23 P:THR515 4.7 5.4 1.0 H P:GLY516 4.8 4.9 1.0 HA P:THR515 4.8 5.4 1.0 HG1 P:THR515 4.8 5.4 1.0 HG1 P:THR750 4.9 4.3 1.0 H P:THR517 4.9 5.2 1.0 HA2 P:GLY516 4.9 4.9 1.0 OD2 P:ASP878 4.9 8.6 1.0

Fluorine binding site 2 out of 4 in the Cryo-Em Structure of ATP13A2 in the Nominal E1P 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 Nominal E1P State within 5.0Å range: probe atom residue distance (Å) B Occ P:F1201 b:3.6 occ:1.00 F2 P:ALF1201 0.0 3.6 1.0 AL P:ALF1201 1.8 3.6 1.0 F3 P:ALF1201 2.5 3.6 1.0 F4 P:ALF1201 2.5 3.6 1.0 HA P:THR750 2.9 4.3 1.0 HZ2 P:LYS859 2.9 9.8 1.0 HD22 P:ASN881 3.0 10.4 1.0 HG1 P:THR750 3.0 4.3 1.0 HB3 P:ASP513 3.2 3.7 1.0 HB2 P:ASP513 3.3 3.7 1.0 H P:GLY751 3.3 3.9 1.0 F1 P:ALF1201 3.6 3.6 1.0 CB P:ASP513 3.7 3.7 1.0 NZ P:LYS859 3.8 9.8 1.0 CA P:THR750 3.8 4.3 1.0 OG1 P:THR750 3.8 4.3 1.0 ND2 P:ASN881 3.9 10.4 1.0 HZ3 P:LYS859 3.9 9.8 1.0 OD2 P:ASP513 4.0 3.7 1.0 N P:GLY751 4.0 3.9 1.0 HA3 P:GLY347 4.1 8.9 1.0 HZ1 P:LYS859 4.1 9.8 1.0 HB P:THR750 4.2 4.3 1.0 CB P:THR750 4.2 4.3 1.0 O P:VAL749 4.3 2.4 1.0 HD21 P:ASN881 4.3 10.4 1.0 CG P:ASP513 4.4 3.7 1.0 H P:GLY347 4.4 8.9 1.0 MG P:MG1202 4.4 16.3 1.0 C P:THR750 4.5 4.3 1.0 HA2 P:GLY347 4.7 8.9 1.0 CA P:GLY347 4.7 8.9 1.0 OD1 P:ASN881 4.8 10.4 1.0 CG P:ASN881 4.8 10.4 1.0 N P:GLY347 4.8 8.9 1.0 HE2 P:LYS859 4.8 9.8 1.0 N P:THR750 4.8 4.3 1.0 CE P:LYS859 4.8 9.8 1.0 HA P:ASP513 4.9 3.7 1.0 C P:VAL749 5.0 2.4 1.0 CA P:ASP513 5.0 3.7 1.0 HE3 P:LYS859 5.0 9.8 1.0 HA3 P:GLY751 5.0 3.9 1.0

Fluorine binding site 3 out of 4 in the Cryo-Em Structure of ATP13A2 in the Nominal E1P 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 Nominal E1P State within 5.0Å range: probe atom residue distance (Å) B Occ P:F1201 b:3.6 occ:1.00 F3 P:ALF1201 0.0 3.6 1.0 AL P:ALF1201 1.8 3.6 1.0 MG P:MG1202 2.2 16.3 1.0 F2 P:ALF1201 2.5 3.6 1.0 F1 P:ALF1201 2.5 3.6 1.0 OD2 P:ASP513 2.6 3.7 1.0 HD22 P:ASN881 3.4 10.4 1.0 F4 P:ALF1201 3.6 3.6 1.0 H P:GLY879 3.6 11.4 1.0 OD1 P:ASN881 3.7 10.4 1.0 CG P:ASP513 3.7 3.7 1.0 HB2 P:ASP513 3.7 3.7 1.0 HB3 P:ASP513 3.8 3.7 1.0 H P:ASP878 3.8 8.6 1.0 CB P:ASP513 3.9 3.7 1.0 HZ2 P:LYS859 4.0 9.8 1.0 OD1 P:ASP878 4.1 8.6 1.0 ND2 P:ASN881 4.1 10.4 1.0 HA3 P:GLY879 4.2 11.4 1.0 HZ3 P:LYS859 4.2 9.8 1.0 CG P:ASN881 4.3 10.4 1.0 HA3 P:GLY877 4.4 5.6 1.0 N P:GLY879 4.4 11.4 1.0 NZ P:LYS859 4.5 9.8 1.0 OD2 P:ASP882 4.6 10.4 1.0 HZ1 P:LYS859 4.6 9.8 1.0 HA2 P:GLY877 4.6 5.6 1.0 N P:ASP878 4.7 8.6 1.0 O P:THR515 4.7 5.4 1.0 OD1 P:ASP513 4.8 3.7 1.0 CA P:GLY879 4.8 11.4 1.0 HA2 P:GLY347 4.8 8.9 1.0 HD21 P:ASN881 4.9 10.4 1.0 HA3 P:GLY347 4.9 8.9 1.0 CA P:GLY877 4.9 5.6 1.0

Fluorine binding site 4 out of 4 in the Cryo-Em Structure of ATP13A2 in the Nominal E1P 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 Nominal E1P State within 5.0Å range: probe atom residue distance (Å) B Occ P:F1201 b:3.6 occ:1.00 F4 P:ALF1201 0.0 3.6 1.0 AL P:ALF1201 1.8 3.6 1.0 HG1 P:THR750 2.4 4.3 1.0 F1 P:ALF1201 2.5 3.6 1.0 F2 P:ALF1201 2.5 3.6 1.0 HB P:THR515 2.7 5.4 1.0 HB2 P:ASP513 2.7 3.7 1.0 HA3 P:GLY347 2.9 8.9 1.0 H P:THR515 3.0 5.4 1.0 OG1 P:THR750 3.1 4.3 1.0 CB P:THR515 3.5 5.4 1.0 F3 P:ALF1201 3.6 3.6 1.0 OG1 P:THR515 3.6 5.4 1.0 CB P:ASP513 3.7 3.7 1.0 HG1 P:THR515 3.7 5.4 1.0 N P:THR515 3.7 5.4 1.0 HB3 P:ASP513 3.8 3.7 1.0 CA P:GLY347 3.9 8.9 1.0 O P:THR515 3.9 5.4 1.0 HB P:THR750 3.9 4.3 1.0 HA2 P:GLY347 4.0 8.9 1.0 H P:GLY751 4.0 3.9 1.0 CA P:THR515 4.0 5.4 1.0 HA P:THR750 4.1 4.3 1.0 CB P:THR750 4.1 4.3 1.0 HG3 P:LYS514 4.1 4.8 1.0 H P:LYS514 4.3 4.8 1.0 HG2 P:LYS514 4.3 4.8 1.0 OD2 P:ASP513 4.3 3.7 1.0 C P:THR515 4.3 5.4 1.0 OD1 P:ASP752 4.3 5.4 1.0 MG P:MG1202 4.3 16.3 1.0 H P:GLY347 4.4 8.9 1.0 CG P:ASP513 4.4 3.7 1.0 N P:LYS514 4.5 4.8 1.0 CA P:THR750 4.6 4.3 1.0 CA P:ASP513 4.6 3.7 1.0 N P:GLY347 4.6 8.9 1.0 C P:ASP513 4.6 3.7 1.0 CG P:LYS514 4.7 4.8 1.0 HA P:ASP513 4.7 3.7 1.0 CG2 P:THR515 4.7 5.4 1.0 N P:GLY751 4.8 3.9 1.0 C P:GLY347 4.8 8.9 1.0 HG23 P:THR515 4.8 5.4 1.0 CG P:ASP752 4.9 5.4 1.0 OD2 P:ASP752 4.9 5.4 1.0 C P:LYS514 4.9 4.8 1.0 HG22 P:THR515 5.0 5.4 1.0 HA P:THR515 5.0 5.4 1.0

J.Mu, C.Xue, L.Fu, Z.Yu, M.Nie, M.Wu, X.Chen, K.Liu, R.Bu, Y.Huang, B.Yang, J.Han, Q.Jiang, K.C.Chan, R.Zhou, H.Li, A.Huang, Y.Wang, Z.Liu. Conformational Cycle of Human Polyamine Transporter ATP13A2. Nat Commun V. 14 1978 2023.
ISSN: ESSN 2041-1723
PubMed: 37031211
DOI: 10.1038/S41467-023-37741-0