Fluorine in PDB 7vpk: Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P State)

The structure of Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P State) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P State) (pdb code 7vpk). 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 the Human ATP13A2 (Spm-Bound E2P State), PDB code: 7vpk:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P 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 ATP13A2 (Spm-Bound E2P State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:58.2 occ:1.00 F1 A:BEF1202 0.0 58.2 1.0 BE A:BEF1202 1.8 58.0 1.0 OD1 A:ASP513 2.5 57.5 1.0 OD2 A:ASP513 2.8 57.5 1.0 F3 A:BEF1202 2.8 58.1 1.0 F2 A:BEF1202 2.8 58.8 1.0 N A:GLY751 2.9 66.6 1.0 CG A:ASP513 3.0 56.6 1.0 CA A:THR750 3.4 63.5 1.0 C A:THR750 3.6 64.8 1.0 NZ A:LYS859 3.6 58.1 1.0 OG1 A:THR750 3.7 64.8 1.0 ND2 A:ASN881 3.7 63.6 1.0 MG A:MG1201 3.8 63.2 1.0 CA A:GLY751 3.9 68.4 1.0 CB A:THR750 4.1 64.2 1.0 O A:VAL749 4.3 59.7 1.0 CB A:ASP513 4.4 55.5 1.0 CE A:LYS859 4.5 58.1 1.0 N A:THR750 4.6 61.7 1.0 O A:THR346 4.6 104.0 1.0 N A:LYS514 4.6 57.4 1.0 O A:THR750 4.7 65.1 1.0 CG A:ASN881 4.8 63.0 1.0 CA A:ASP513 4.9 54.7 1.0 C A:VAL749 4.9 59.9 1.0 C A:GLY751 4.9 70.2 1.0

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P 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 ATP13A2 (Spm-Bound E2P State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:58.8 occ:1.00 F2 A:BEF1202 0.0 58.8 1.0 BE A:BEF1202 1.7 58.0 1.0 MG A:MG1201 1.8 63.2 1.0 OD2 A:ASP513 2.8 57.5 1.0 F3 A:BEF1202 2.8 58.1 1.0 F1 A:BEF1202 2.8 58.2 1.0 O A:GLY347 3.1 111.8 1.0 O A:THR515 3.3 62.1 1.0 CB A:THR515 3.4 61.6 1.0 CA A:GLY347 3.5 108.8 1.0 N A:THR515 3.7 60.9 1.0 C A:GLY347 3.8 111.8 1.0 CG A:ASP513 3.8 56.6 1.0 CA A:THR515 3.9 61.6 1.0 OG1 A:THR515 4.0 61.4 1.0 OD1 A:ASP513 4.0 57.5 1.0 C A:THR515 4.0 62.5 1.0 OD2 A:ASP878 4.1 58.1 1.0 O A:THR346 4.1 104.0 1.0 OD1 A:ASP878 4.3 58.1 1.0 CG2 A:THR515 4.4 61.9 1.0 CG A:ASP878 4.5 57.8 1.0 N A:GLY347 4.5 106.3 1.0 OD1 A:ASP752 4.6 78.2 1.0 C A:THR346 4.7 103.7 1.0 C A:LYS514 4.9 60.1 1.0 OG1 A:THR750 4.9 64.8 1.0

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P 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 ATP13A2 (Spm-Bound E2P State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:58.1 occ:1.00 F3 A:BEF1202 0.0 58.1 1.0 BE A:BEF1202 1.7 58.0 1.0 OG1 A:THR750 2.6 64.8 1.0 N A:THR515 2.7 60.9 1.0 OD2 A:ASP513 2.8 57.5 1.0 F2 A:BEF1202 2.8 58.8 1.0 F1 A:BEF1202 2.8 58.2 1.0 N A:LYS514 3.1 57.4 1.0 CB A:LYS514 3.2 58.9 1.0 CA A:LYS514 3.3 58.8 1.0 CB A:THR750 3.4 64.2 1.0 C A:LYS514 3.4 60.1 1.0 OG1 A:THR515 3.6 61.4 1.0 CG A:ASP513 3.7 56.6 1.0 CA A:THR515 3.7 61.6 1.0 CB A:THR515 3.8 61.6 1.0 CA A:THR750 3.9 63.5 1.0 MG A:MG1201 4.0 63.2 1.0 CG A:LYS514 4.0 59.1 1.0 CD A:LYS514 4.0 59.5 1.0 OD1 A:ASP513 4.1 57.5 1.0 N A:GLY751 4.1 66.6 1.0 C A:ASP513 4.3 56.1 1.0 OD1 A:ASP752 4.3 78.2 1.0 O A:THR515 4.4 62.1 1.0 CG A:ASP752 4.6 77.8 1.0 C A:THR750 4.6 64.8 1.0 C A:THR515 4.6 62.5 1.0 O A:LYS514 4.6 61.0 1.0 CB A:ASP513 4.7 55.5 1.0 CA A:ASP513 4.7 54.7 1.0 CG2 A:THR750 4.7 64.2 1.0 CB A:ASP752 4.9 76.6 1.0

A.Tomita, T.Daiho, T.Kusakizako, K.Yamashita, S.Ogasawara, T.Murata, T.Nishizawa, O.Nureki. Cryo-Em Reveals Mechanistic Insights Into Lipid-Facilitated Polyamine Export By Human ATP13A2. Mol.Cell V. 81 4799 2021.
ISSN: ISSN 1097-2765
PubMed: 34798056
DOI: 10.1016/J.MOLCEL.2021.11.001