Fluorine in PDB 8ijl: Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp

The structure of Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Aluminium	(Al)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Fluorine atom in the Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp (pdb code 8ijl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp, PDB code: 8ijl:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:43.6 occ:1.00 F1 A:ALF1101 0.0 43.6 1.0 AL A:ALF1101 1.8 37.1 1.0 F3 A:ALF1101 2.5 35.6 1.0 F4 A:ALF1101 2.5 33.7 1.0 ND2 A:ASN732 2.7 27.5 1.0 OD1 A:ASN732 2.8 27.2 1.0 OD1 A:ASP388 3.0 35.7 1.0 OD2 A:ASP733 3.1 36.9 1.0 CG A:ASN732 3.1 24.5 1.0 CG A:ASP388 3.4 24.5 1.0 OD1 A:ASP733 3.4 32.9 1.0 CG A:ASP733 3.5 31.1 1.0 OD2 A:ASP388 3.6 21.1 1.0 MG A:MG1102 3.6 30.3 1.0 F2 A:ALF1101 3.6 16.2 1.0 NZ A:LYS710 3.6 20.6 1.0 CA A:GLY232 3.7 20.9 1.0 O A:HOH1201 3.7 22.0 1.0 O A:THR231 4.1 36.0 1.0 N A:GLY232 4.3 12.8 1.0 CB A:ASP388 4.4 18.3 1.0 C A:THR231 4.5 18.9 1.0 CE A:LYS710 4.5 25.8 1.0 CB A:ASN732 4.6 27.2 1.0 C A:GLY232 4.7 21.3 1.0 O A:GLY232 4.9 27.3 1.0 CA A:GLY730 4.9 30.7 1.0 N A:ASP733 4.9 28.1 1.0 CB A:ASP733 4.9 22.1 1.0

Fluorine binding site 2 out of 4 in the Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:16.2 occ:1.00 F2 A:ALF1101 0.0 16.2 1.0 AL A:ALF1101 1.8 37.1 1.0 OD1 A:ASP388 1.9 35.7 1.0 O A:HOH1201 2.2 22.0 1.0 F4 A:ALF1101 2.5 33.7 1.0 F3 A:ALF1101 2.6 35.6 1.0 OG1 A:THR629 2.7 28.5 1.0 CG A:ASP388 3.0 24.5 1.0 N A:THR390 3.1 22.8 1.0 N A:LYS389 3.3 20.9 1.0 OD2 A:ASP388 3.5 21.1 1.0 F1 A:ALF1101 3.6 43.6 1.0 CB A:THR390 3.7 24.7 1.0 CB A:THR629 3.8 21.5 1.0 OG1 A:THR390 3.8 28.3 1.0 OE2 A:GLU233 3.8 31.8 1.0 CA A:LYS389 3.9 18.2 1.0 C A:LYS389 3.9 19.5 1.0 CA A:THR390 3.9 19.7 1.0 CA A:THR629 4.0 23.4 1.0 CB A:LYS389 4.0 25.9 1.0 N A:GLY630 4.0 20.2 1.0 CB A:ASP388 4.2 18.3 1.0 C A:ASP388 4.2 24.4 1.0 O A:THR390 4.3 34.4 1.0 MG A:MG1102 4.3 30.3 1.0 CA A:ASP388 4.4 17.2 1.0 C A:THR629 4.6 23.5 1.0 NZ A:LYS710 4.6 20.6 1.0 C A:THR390 4.6 23.4 1.0 O A:THR231 4.6 36.0 1.0 O A:VAL628 4.8 25.9 1.0

Fluorine binding site 3 out of 4 in the Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:35.6 occ:1.00 F3 A:ALF1101 0.0 35.6 1.0 AL A:ALF1101 1.8 37.1 1.0 MG A:MG1102 1.8 30.3 1.0 OD2 A:ASP388 2.3 21.1 1.0 OD1 A:ASP388 2.4 35.7 1.0 F1 A:ALF1101 2.5 43.6 1.0 F2 A:ALF1101 2.6 16.2 1.0 CG A:ASP388 2.7 24.5 1.0 O A:THR390 2.7 34.4 1.0 O A:HOH1201 3.3 22.0 1.0 F4 A:ALF1101 3.6 33.7 1.0 CB A:THR390 3.6 24.7 1.0 C A:THR390 3.6 23.4 1.0 N A:THR390 3.7 22.8 1.0 OD1 A:ASP729 3.7 33.2 1.0 CA A:THR390 3.8 19.7 1.0 O A:GLY232 3.9 27.3 1.0 CA A:GLY232 4.1 20.9 1.0 CB A:ASP388 4.2 18.3 1.0 OD2 A:ASP733 4.3 36.9 1.0 C A:GLY232 4.4 21.3 1.0 OG1 A:THR390 4.5 28.3 1.0 CG2 A:THR390 4.5 24.3 1.0 C A:LYS389 4.6 19.5 1.0 OE2 A:GLU233 4.7 31.8 1.0 N A:LYS389 4.7 20.9 1.0 CG A:ASP729 4.8 26.5 1.0 N A:GLY391 4.9 23.9 1.0 OD1 A:ASN732 4.9 27.2 1.0 O A:THR231 4.9 36.0 1.0

Fluorine binding site 4 out of 4 in the Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cyo-Em Structure of Wildtype Non-Gastric Proton Pump in the Presence of Na+, Alf and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:33.7 occ:1.00 F4 A:ALF1101 0.0 33.7 1.0 AL A:ALF1101 1.8 37.1 1.0 OD1 A:ASP388 2.5 35.7 1.0 F2 A:ALF1101 2.5 16.2 1.0 F1 A:ALF1101 2.5 43.6 1.0 NZ A:LYS710 2.6 20.6 1.0 O A:HOH1201 2.7 22.0 1.0 N A:GLY630 3.0 20.2 1.0 CE A:LYS710 3.2 25.8 1.0 ND2 A:ASN732 3.3 27.5 1.0 CA A:THR629 3.5 23.4 1.0 F3 A:ALF1101 3.6 35.6 1.0 CG A:ASP388 3.6 24.5 1.0 C A:THR629 3.7 23.5 1.0 O A:THR231 3.8 36.0 1.0 OG1 A:THR629 3.8 28.5 1.0 CA A:GLY630 4.0 16.5 1.0 OD1 A:ASP733 4.1 32.9 1.0 O A:VAL628 4.1 25.9 1.0 CB A:THR629 4.3 21.5 1.0 CB A:ASP388 4.4 18.3 1.0 CG A:ASN732 4.4 24.5 1.0 OD2 A:ASP388 4.4 21.1 1.0 N A:THR629 4.6 24.3 1.0 CD A:LYS710 4.6 25.0 1.0 C A:THR231 4.7 18.9 1.0 OD1 A:ASN732 4.7 27.2 1.0 C A:VAL628 4.8 19.8 1.0 O A:THR629 4.8 31.1 1.0 CA A:ASP388 4.9 17.2 1.0 OD2 A:ASP733 4.9 36.9 1.0 CA A:GLY232 4.9 20.9 1.0 CG A:ASP733 4.9 31.1 1.0 N A:LYS389 4.9 20.9 1.0 C A:GLY630 5.0 29.6 1.0

K.Abe, T.Nishizawa, P.Artigas. An Unusual Conformation From Na + -Sensitive Non-Gastric Proton Pump Mutants Reveals Molecular Mechanisms of Cooperative Na + -Binding. Biochim Biophys Acta Mol V.1870 19543 2023CELL Res.
ISSN: ISSN 1879-2596
PubMed: 37482134
DOI: 10.1016/J.BBAMCR.2023.119543