Fluorine in PDB 7vpj: Cryo-Em Structure of the Human ATP13A2 (E1P-Adp State)

The structure of Cryo-Em Structure of the Human ATP13A2 (E1P-Adp 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 (E1P-Adp State) (pdb code 7vpj). 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 (E1P-Adp State), PDB code: 7vpj:
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 (E1P-Adp 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 (E1P-Adp State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1204 b:88.2 occ:1.00 F1 A:ALF1204 0.0 88.2 1.0 AL A:ALF1204 1.8 88.2 1.0 F3 A:ALF1204 2.3 88.5 1.0 O2B A:ADP1202 2.3 80.6 1.0 OG1 A:THR515 2.5 74.4 1.0 F4 A:ALF1204 2.6 87.0 1.0 OD2 A:ASP513 2.7 69.4 1.0 MG A:MG1201 3.1 139.2 1.0 O A:THR515 3.1 73.8 1.0 CG A:ASP513 3.2 67.4 1.0 OD1 A:ASP513 3.3 69.5 1.0 N A:THR515 3.4 71.8 1.0 F2 A:ALF1204 3.6 89.0 1.0 PB A:ADP1202 3.6 81.1 1.0 CB A:THR515 3.6 73.9 1.0 CA A:THR515 3.8 73.3 1.0 C A:THR515 3.9 74.8 1.0 O3B A:ADP1202 3.9 82.7 1.0 O3A A:ADP1202 4.3 82.5 1.0 CG2 A:THR515 4.3 73.6 1.0 ND2 A:ASN881 4.4 93.9 1.0 N A:LYS514 4.5 66.5 1.0 CB A:ASP513 4.5 65.2 1.0 C A:LYS514 4.6 70.1 1.0 O1B A:ADP1202 4.7 82.0 1.0 OD1 A:ASN881 4.8 94.6 1.0 CA A:LYS514 5.0 67.7 1.0

Fluorine binding site 2 out of 4 in the Cryo-Em Structure of the Human ATP13A2 (E1P-Adp 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 (E1P-Adp State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1204 b:89.0 occ:1.00 F2 A:ALF1204 0.0 89.0 1.0 AL A:ALF1204 1.8 88.2 1.0 NZ A:LYS859 2.5 111.2 1.0 F4 A:ALF1204 2.6 87.0 1.0 F3 A:ALF1204 2.6 88.5 1.0 ND2 A:ASN881 3.0 93.9 1.0 CA A:THR750 3.3 63.0 1.0 OD2 A:ASP513 3.4 69.4 1.0 N A:GLY751 3.5 68.7 1.0 O A:VAL749 3.5 66.0 1.0 F1 A:ALF1204 3.6 88.2 1.0 CG A:ASP513 3.8 67.4 1.0 C A:THR750 3.8 65.4 1.0 CE A:LYS859 3.8 111.3 1.0 CB A:ASP513 3.9 65.2 1.0 O2B A:ADP1202 3.9 80.6 1.0 N A:THR750 4.1 63.2 1.0 OD2 A:ASP882 4.2 98.4 1.0 C A:VAL749 4.2 63.5 1.0 CB A:THR750 4.3 62.9 1.0 CG A:ASN881 4.3 94.7 1.0 CD A:LYS859 4.4 112.8 1.0 CA A:ASP513 4.4 65.4 1.0 O3A A:ADP1202 4.5 82.5 1.0 N A:LYS514 4.5 66.5 1.0 OD1 A:ASP513 4.6 69.5 1.0 CA A:GLY751 4.7 71.3 1.0 O A:THR750 4.9 67.7 1.0 PB A:ADP1202 4.9 81.1 1.0 OD1 A:ASP882 4.9 96.5 1.0 CG A:ASP882 5.0 96.9 1.0 OD1 A:ASN881 5.0 94.6 1.0

Fluorine binding site 3 out of 4 in the Cryo-Em Structure of the Human ATP13A2 (E1P-Adp 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 (E1P-Adp State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1204 b:88.5 occ:1.00 F3 A:ALF1204 0.0 88.5 1.0 AL A:ALF1204 1.8 88.2 1.0 ND2 A:ASN881 2.1 93.9 1.0 F1 A:ALF1204 2.3 88.2 1.0 OD2 A:ASP513 2.6 69.4 1.0 F2 A:ALF1204 2.6 89.0 1.0 CG A:ASN881 2.8 94.7 1.0 OD1 A:ASN881 2.9 94.6 1.0 MG A:MG1201 3.1 139.2 1.0 O2B A:ADP1202 3.4 80.6 1.0 F4 A:ALF1204 3.6 87.0 1.0 CG A:ASP513 3.6 67.4 1.0 OD1 A:ASP882 3.8 96.5 1.0 O3A A:ADP1202 4.0 82.5 1.0 NZ A:LYS859 4.1 111.2 1.0 CB A:ASN881 4.2 95.8 1.0 PB A:ADP1202 4.2 81.1 1.0 OD2 A:ASP882 4.3 98.4 1.0 OD1 A:ASP513 4.4 69.5 1.0 O2A A:ADP1202 4.4 84.8 1.0 CG A:ASP882 4.4 96.9 1.0 CB A:ASP513 4.5 65.2 1.0 O3B A:ADP1202 4.6 82.7 1.0 OG1 A:THR515 4.7 74.4 1.0 PA A:ADP1202 4.7 84.5 1.0 O A:THR515 4.9 73.8 1.0

Fluorine binding site 4 out of 4 in the Cryo-Em Structure of the Human ATP13A2 (E1P-Adp 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 (E1P-Adp State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1204 b:87.0 occ:1.00 F4 A:ALF1204 0.0 87.0 1.0 AL A:ALF1204 1.8 88.2 1.0 F2 A:ALF1204 2.6 89.0 1.0 F1 A:ALF1204 2.6 88.2 1.0 N A:LYS514 2.8 66.5 1.0 O2B A:ADP1202 2.9 80.6 1.0 CB A:LYS514 3.2 66.8 1.0 N A:THR515 3.3 71.8 1.0 CA A:LYS514 3.4 67.7 1.0 CG A:ASP513 3.4 67.4 1.0 OD2 A:ASP513 3.5 69.4 1.0 OD1 A:ASP513 3.5 69.5 1.0 F3 A:ALF1204 3.6 88.5 1.0 CB A:THR750 3.8 62.9 1.0 CA A:THR750 3.8 63.0 1.0 C A:ASP513 3.8 65.9 1.0 C A:LYS514 3.8 70.1 1.0 CB A:ASP513 4.0 65.2 1.0 CA A:ASP513 4.0 65.4 1.0 OG1 A:THR515 4.1 74.4 1.0 CG2 A:THR750 4.1 62.7 1.0 N A:GLY751 4.3 68.7 1.0 PB A:ADP1202 4.3 81.1 1.0 O A:VAL749 4.4 66.0 1.0 CA A:THR515 4.5 73.3 1.0 C A:THR750 4.6 65.4 1.0 CB A:THR515 4.6 73.9 1.0 CG2 A:THR515 4.6 73.6 1.0 CG A:LYS514 4.7 66.5 1.0 O3A A:ADP1202 4.8 82.5 1.0 O A:THR515 4.8 73.8 1.0 O1B A:ADP1202 4.9 82.0 1.0 NZ A:LYS859 4.9 111.2 1.0 N A:THR750 4.9 63.2 1.0 O A:ASP513 4.9 67.2 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