Fluorine in PDB 7vpl: Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2PI State)

The structure of Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2PI 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 ATP13A2 (Spm-Bound E2PI State) (pdb code 7vpl). 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 ATP13A2 (Spm-Bound E2PI State), PDB code: 7vpl:
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 ATP13A2 (Spm-Bound E2PI 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 E2PI State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:67.6 occ:1.00 F1 A:ALF1202 0.0 67.6 1.0 AL A:ALF1202 1.8 67.1 1.0 F4 A:ALF1202 2.5 67.2 1.0 F3 A:ALF1202 2.6 66.8 1.0 OD1 A:ASP513 2.7 63.9 1.0 OG1 A:THR750 2.9 67.5 1.0 N A:THR515 3.1 70.8 1.0 N A:LYS514 3.1 64.2 1.0 CB A:LYS514 3.3 66.1 1.0 CA A:LYS514 3.6 66.1 1.0 CB A:THR750 3.6 67.4 1.0 F2 A:ALF1202 3.6 67.4 1.0 CG A:ASP513 3.6 63.4 1.0 CA A:THR750 3.7 67.5 1.0 OG1 A:THR515 3.8 74.2 1.0 C A:LYS514 3.8 68.3 1.0 OE2 A:GLU348 3.9 128.1 1.0 CB A:THR515 4.0 74.1 1.0 N A:GLY751 4.0 73.5 1.0 CA A:THR515 4.1 73.2 1.0 OD2 A:ASP513 4.1 63.7 1.0 C A:ASP513 4.2 62.5 1.0 C A:THR750 4.4 70.2 1.0 MG A:MG1201 4.4 55.8 1.0 CG A:LYS514 4.5 66.5 1.0 CA A:ASP513 4.6 61.5 1.0 CE A:LYS514 4.6 67.6 1.0 OE1 A:GLU348 4.7 128.4 1.0 CB A:ASP513 4.7 62.7 1.0 O A:VAL749 4.7 63.2 1.0 CD A:GLU348 4.7 128.4 1.0 CD A:LYS514 4.8 67.2 1.0 O A:THR515 4.9 74.8 1.0 N A:THR750 4.9 65.0 1.0 CG2 A:THR750 5.0 67.7 1.0

Fluorine binding site 2 out of 4 in the Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2PI 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 E2PI State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:67.4 occ:1.00 F2 A:ALF1202 0.0 67.4 1.0 AL A:ALF1202 1.8 67.1 1.0 F3 A:ALF1202 2.5 66.8 1.0 F4 A:ALF1202 2.5 67.2 1.0 OD1 A:ASP513 2.6 63.9 1.0 ND2 A:ASN881 3.2 75.9 1.0 MG A:MG1201 3.2 55.8 1.0 CG A:ASP513 3.4 63.4 1.0 F1 A:ALF1202 3.6 67.6 1.0 CA A:GLY347 3.7 115.8 1.0 OD2 A:ASP513 3.8 63.7 1.0 O A:THR346 3.9 108.0 1.0 CB A:ASN881 4.0 74.4 1.0 CG A:ASN881 4.1 75.2 1.0 OD2 A:ASP882 4.2 77.0 1.0 N A:GLY347 4.4 112.4 1.0 O A:GLY347 4.4 119.7 1.0 C A:THR346 4.5 108.9 1.0 C A:GLY347 4.5 119.5 1.0 CB A:ASP513 4.6 62.7 1.0 NZ A:LYS859 4.6 65.6 1.0 CE A:LYS859 4.7 65.8 1.0 OE2 A:GLU348 4.7 128.1 1.0 OD1 A:ASP878 4.9 67.4 1.0 N A:GLY751 4.9 73.5 1.0

Fluorine binding site 3 out of 4 in the Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2PI 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 E2PI State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:66.8 occ:1.00 F3 A:ALF1202 0.0 66.8 1.0 AL A:ALF1202 1.8 67.1 1.0 MG A:MG1201 2.0 55.8 1.0 F2 A:ALF1202 2.5 67.4 1.0 OD1 A:ASP513 2.6 63.9 1.0 F1 A:ALF1202 2.6 67.6 1.0 OD2 A:ASP513 2.9 63.7 1.0 O A:THR515 3.0 74.8 1.0 CG A:ASP513 3.1 63.4 1.0 CB A:THR515 3.2 74.1 1.0 N A:THR515 3.2 70.8 1.0 CA A:THR515 3.4 73.2 1.0 F4 A:ALF1202 3.6 67.2 1.0 C A:THR515 3.7 74.9 1.0 O A:GLY347 3.7 119.7 1.0 OG1 A:THR515 3.9 74.2 1.0 OD1 A:ASP878 4.2 67.4 1.0 CG2 A:THR515 4.2 74.6 1.0 CA A:GLY347 4.3 115.8 1.0 C A:LYS514 4.3 68.3 1.0 C A:GLY347 4.4 119.5 1.0 N A:LYS514 4.4 64.2 1.0 OE2 A:GLU348 4.5 128.1 1.0 CB A:ASP513 4.6 62.7 1.0 OE1 A:GLU348 4.8 128.4 1.0 CA A:LYS514 4.9 66.1 1.0 N A:GLY516 5.0 76.7 1.0

Fluorine binding site 4 out of 4 in the Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2PI 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 ATP13A2 (Spm-Bound E2PI State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:67.2 occ:1.00 F4 A:ALF1202 0.0 67.2 1.0 AL A:ALF1202 1.8 67.1 1.0 F1 A:ALF1202 2.5 67.6 1.0 F2 A:ALF1202 2.5 67.4 1.0 N A:GLY751 2.6 73.5 1.0 OD1 A:ASP513 2.7 63.9 1.0 NZ A:LYS859 2.9 65.6 1.0 CA A:THR750 3.2 67.5 1.0 C A:THR750 3.3 70.2 1.0 ND2 A:ASN881 3.5 75.9 1.0 F3 A:ALF1202 3.6 66.8 1.0 OG1 A:THR750 3.6 67.5 1.0 CA A:GLY751 3.7 77.1 1.0 CE A:LYS859 3.8 65.8 1.0 O A:THR346 3.9 108.0 1.0 CG A:ASP513 3.9 63.4 1.0 CB A:THR750 4.0 67.4 1.0 O A:VAL749 4.1 63.2 1.0 OE2 A:GLU348 4.2 128.1 1.0 N A:THR750 4.3 65.0 1.0 O A:THR750 4.5 71.2 1.0 C A:VAL749 4.6 62.5 1.0 C A:GLY751 4.7 81.2 1.0 N A:LYS514 4.7 64.2 1.0 CB A:ASP513 4.7 62.7 1.0 CG A:ASN881 4.8 75.2 1.0 OD2 A:ASP513 4.8 63.7 1.0 CD A:LYS859 4.8 66.2 1.0 CA A:ASP513 4.9 61.5 1.0 N A:ASP752 4.9 85.5 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