Fluorine in PDB 8wa5: Cryo-Em Structure of the Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf State

The structure of Cryo-Em Structure of the Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf State also contains other interesting chemical elements:

Aluminium	(Al)	1 atom
Potassium	(K)	3 atoms
Magnesium	(Mg)	1 atom

The binding sites of Fluorine atom in the Cryo-Em Structure of the Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf State (pdb code 8wa5). 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 Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf State, PDB code: 8wa5:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf 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 Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1104 b:39.9 occ:1.00 F1 A:ALF1104 0.0 39.9 1.0 AL A:ALF1104 1.8 39.9 1.0 F4 A:ALF1104 2.5 39.9 1.0 F3 A:ALF1104 2.6 39.9 1.0 OD1 A:ASP385 2.7 33.2 1.0 NZ A:LYS707 2.8 35.2 1.0 N A:GLY627 2.9 39.5 1.0 O A:THR228 3.2 46.9 1.0 ND2 A:ASN729 3.3 40.2 1.0 F2 A:ALF1104 3.6 39.9 1.0 CE A:LYS707 3.7 35.2 1.0 CA A:THR626 3.7 36.5 1.0 C A:THR626 3.7 36.5 1.0 CA A:GLY627 3.7 39.5 1.0 CG A:ASP385 3.8 33.2 1.0 OG1 A:THR626 3.9 36.5 1.0 C A:THR228 4.2 46.9 1.0 O A:HOH1204 4.3 37.8 1.0 OD2 A:ASP385 4.3 33.2 1.0 CB A:THR626 4.3 36.5 1.0 OD1 A:ASP730 4.5 35.9 1.0 CA A:GLY229 4.5 44.6 1.0 O A:VAL625 4.6 33.2 1.0 CG A:ASN729 4.6 40.2 1.0 C A:GLY627 4.7 39.5 1.0 N A:GLY229 4.7 44.6 1.0 OE2 A:GLU230 4.8 48.5 1.0 O A:THR626 4.8 36.5 1.0 N A:THR626 4.8 36.5 1.0 N A:ASP628 4.9 43.5 1.0 OD2 A:ASP730 5.0 35.9 1.0

Fluorine binding site 2 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf 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 Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1104 b:39.9 occ:1.00 F2 A:ALF1104 0.0 39.9 1.0 AL A:ALF1104 1.8 39.9 1.0 MG A:MG1105 1.9 35.3 1.0 F3 A:ALF1104 2.5 39.9 1.0 F4 A:ALF1104 2.6 39.9 1.0 OD2 A:ASP385 2.6 33.2 1.0 O A:THR387 2.9 38.4 1.0 OD1 A:ASP385 3.3 33.2 1.0 CB A:THR387 3.3 38.4 1.0 CG A:ASP385 3.3 33.2 1.0 O A:GLY229 3.3 44.6 1.0 CA A:GLY229 3.5 44.6 1.0 F1 A:ALF1104 3.6 39.9 1.0 C A:THR387 3.6 38.4 1.0 CA A:THR387 3.7 38.4 1.0 N A:THR387 3.8 38.4 1.0 C A:GLY229 3.8 44.6 1.0 OD1 A:ASP726 3.9 37.5 1.0 OG1 A:THR387 4.0 38.4 1.0 CG2 A:THR387 4.2 38.4 1.0 OD2 A:ASP730 4.3 35.9 1.0 OE2 A:GLU230 4.5 48.5 1.0 O A:THR228 4.6 46.9 1.0 ND2 A:ASN729 4.7 40.2 1.0 N A:GLY229 4.8 44.6 1.0 CB A:ASP385 4.8 33.2 1.0 C A:LYS386 4.9 36.1 1.0 N A:GLY388 4.9 36.4 1.0 CG A:ASP726 5.0 37.5 1.0

Fluorine binding site 3 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf 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 Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1104 b:39.9 occ:1.00 F3 A:ALF1104 0.0 39.9 1.0 AL A:ALF1104 1.8 39.9 1.0 ND2 A:ASN729 2.2 40.2 1.0 F2 A:ALF1104 2.5 39.9 1.0 F1 A:ALF1104 2.6 39.9 1.0 CG A:ASN729 3.1 40.2 1.0 OD2 A:ASP730 3.1 35.9 1.0 OD1 A:ASN729 3.2 40.2 1.0 CA A:GLY229 3.2 44.6 1.0 OD1 A:ASP385 3.3 33.2 1.0 OD2 A:ASP385 3.5 33.2 1.0 NZ A:LYS707 3.5 35.2 1.0 MG A:MG1105 3.6 35.3 1.0 F4 A:ALF1104 3.6 39.9 1.0 CG A:ASP385 3.6 33.2 1.0 OD1 A:ASP730 3.6 35.9 1.0 CG A:ASP730 3.7 35.9 1.0 O A:THR228 3.7 46.9 1.0 N A:GLY229 3.9 44.6 1.0 C A:THR228 4.1 46.9 1.0 C A:GLY229 4.4 44.6 1.0 CB A:ASN729 4.5 40.2 1.0 O A:GLY229 4.6 44.6 1.0 CE A:LYS707 4.8 35.2 1.0 O A:HOH1204 4.8 37.8 1.0 N A:ASP730 4.9 35.9 1.0 CA A:GLY727 4.9 39.4 1.0 CB A:ASP385 4.9 33.2 1.0 CB A:ASP730 5.0 35.9 1.0

Fluorine binding site 4 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf 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 Gastric Proton Pump Y799W/E936Q Mutant in K+- Occluded (K+)E2-Alf State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1104 b:39.9 occ:1.00 F4 A:ALF1104 0.0 39.9 1.0 AL A:ALF1104 1.8 39.9 1.0 F1 A:ALF1104 2.5 39.9 1.0 F2 A:ALF1104 2.6 39.9 1.0 OD1 A:ASP385 2.7 33.2 1.0 OG1 A:THR387 3.1 38.4 1.0 N A:THR387 3.1 38.4 1.0 OG1 A:THR626 3.1 36.5 1.0 OE2 A:GLU230 3.3 48.5 1.0 CB A:THR387 3.3 38.4 1.0 CG A:ASP385 3.5 33.2 1.0 F3 A:ALF1104 3.6 39.9 1.0 OD2 A:ASP385 3.7 33.2 1.0 CA A:THR387 3.8 38.4 1.0 N A:LYS386 3.9 36.1 1.0 N A:GLY627 4.0 39.5 1.0 CB A:THR626 4.0 36.5 1.0 C A:LYS386 4.1 36.1 1.0 CB A:LYS386 4.2 36.1 1.0 MG A:MG1105 4.2 35.3 1.0 O A:THR228 4.2 46.9 1.0 CA A:LYS386 4.2 36.1 1.0 O A:THR387 4.3 38.4 1.0 CA A:THR626 4.3 36.5 1.0 CD A:GLU230 4.5 48.5 1.0 O A:GLY229 4.5 44.6 1.0 C A:THR387 4.5 38.4 1.0 CA A:GLY229 4.7 44.6 1.0 CG2 A:THR387 4.7 38.4 1.0 C A:THR626 4.7 36.5 1.0 C A:GLY229 4.8 44.6 1.0 CE A:LYS386 4.8 36.1 1.0 CB A:ASP385 4.9 33.2 1.0 C A:ASP385 4.9 33.2 1.0 N A:ASP628 4.9 43.5 1.0 CA A:GLY627 4.9 39.5 1.0 NZ A:LYS707 4.9 35.2 1.0

H.V.Madapally, K.Abe, V.Dubey, H.Khandelia. Specific Protonation of Acidic Residues Confers K+ Selectivity to the Gastric Proton Pump. To Be Published.