Fluorine in PDB 6jxj: Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP)

All present enzymatic activity of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP):
7.2.2.19;

The structure of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxj was solved by K.Abe, K.Irie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.71 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.230, 103.230, 369.440, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 27.3

The structure of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP) also contains other interesting chemical elements:

Rubidium	(Rb)	8 atoms
Magnesium	(Mg)	1 atom
Aluminium	(Al)	1 atom

The binding sites of Fluorine atom in the Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP) (pdb code 6jxj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxj:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1107 b:41.3 occ:1.00 F1 A:ALF1107 0.0 41.3 1.0 AL A:ALF1107 1.8 35.0 1.0 O A:HOH1238 2.5 31.4 1.0 F4 A:ALF1107 2.5 43.0 1.0 F3 A:ALF1107 2.6 39.0 1.0 OD1 A:ASP385 2.6 50.8 1.0 ND2 A:ASN729 2.7 28.1 1.0 O A:HOH1219 2.9 44.8 1.0 CA A:GLY229 3.0 29.6 1.0 CG A:ASP385 3.2 43.7 1.0 OD2 A:ASP385 3.2 26.6 1.0 OD1 A:ASN729 3.4 43.1 1.0 CG A:ASN729 3.5 28.7 1.0 F2 A:ALF1107 3.6 34.2 1.0 O A:THR228 3.6 41.4 1.0 MG A:MG1101 3.7 33.7 1.0 N A:GLY229 3.8 37.9 1.0 NZ A:LYS707 3.8 35.6 1.0 C A:THR228 4.0 39.6 1.0 C A:GLY229 4.0 41.2 1.0 OD2 A:ASP730 4.2 47.8 1.0 O A:GLY229 4.2 58.1 1.0 OD1 A:ASP730 4.2 30.2 1.0 CB A:ASP385 4.4 36.1 1.0 CG A:ASP730 4.5 42.5 1.0 OD1 A:ASP726 4.8 40.2 1.0 O A:THR387 4.9 37.3 1.0 CE A:LYS707 5.0 37.0 1.0 CB A:ASN729 5.0 22.9 1.0

Fluorine binding site 2 out of 4 in the Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1107 b:34.2 occ:1.00 F2 A:ALF1107 0.0 34.2 1.0 AL A:ALF1107 1.8 35.0 1.0 OD1 A:ASP385 2.0 50.8 1.0 F4 A:ALF1107 2.5 43.0 1.0 F3 A:ALF1107 2.6 39.0 1.0 OG1 A:THR626 2.8 46.1 1.0 N A:THR387 2.8 39.3 1.0 O A:HOH1219 2.9 44.8 1.0 N A:LYS386 2.9 39.1 1.0 CG A:ASP385 3.0 43.7 1.0 CB A:THR626 3.2 41.4 1.0 CA A:LYS386 3.4 36.4 1.0 CB A:LYS386 3.5 34.9 1.0 C A:LYS386 3.5 36.5 1.0 F1 A:ALF1107 3.6 41.3 1.0 OD2 A:ASP385 3.6 26.6 1.0 CA A:THR626 3.7 40.9 1.0 OG1 A:THR387 3.7 52.7 1.0 C A:ASP385 3.8 40.0 1.0 CB A:THR387 3.8 48.3 1.0 CA A:THR387 3.8 44.3 1.0 OE1 A:GLU230 4.1 46.6 1.0 N A:GLY627 4.1 29.9 1.0 CB A:ASP385 4.1 36.1 1.0 CA A:ASP385 4.2 22.3 1.0 C A:THR626 4.4 44.7 1.0 O A:THR387 4.5 37.3 1.0 CG A:LYS386 4.6 36.3 1.0 CE A:LYS386 4.6 40.9 1.0 NZ A:LYS707 4.6 35.6 1.0 CG2 A:THR626 4.7 27.6 1.0 C A:THR387 4.7 35.7 1.0 O A:LYS386 4.7 36.2 1.0 O A:VAL625 4.7 36.9 1.0 O A:HOH1238 4.7 31.4 1.0 O A:ASP385 4.8 40.4 1.0 N A:THR626 4.8 43.3 1.0 N A:ASP628 4.9 36.1 1.0 MG A:MG1101 4.9 33.7 1.0 O A:THR228 5.0 41.4 1.0

Fluorine binding site 3 out of 4 in the Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1107 b:39.0 occ:1.00 F3 A:ALF1107 0.0 39.0 1.0 AL A:ALF1107 1.8 35.0 1.0 OD2 A:ASP385 2.4 26.6 1.0 MG A:MG1101 2.4 33.7 1.0 OD1 A:ASP385 2.4 50.8 1.0 O A:HOH1238 2.5 31.4 1.0 F2 A:ALF1107 2.6 34.2 1.0 F1 A:ALF1107 2.6 41.3 1.0 O A:THR387 2.6 37.3 1.0 CG A:ASP385 2.7 43.7 1.0 CB A:THR387 2.9 48.3 1.0 N A:THR387 3.0 39.3 1.0 CA A:THR387 3.1 44.3 1.0 C A:THR387 3.2 35.7 1.0 O A:HOH1219 3.3 44.8 1.0 F4 A:ALF1107 3.6 43.0 1.0 OG1 A:THR387 3.7 52.7 1.0 OD1 A:ASP726 3.8 40.2 1.0 O A:GLY229 3.8 58.1 1.0 CG2 A:THR387 4.0 45.2 1.0 C A:LYS386 4.2 36.5 1.0 CA A:GLY229 4.2 29.6 1.0 CB A:ASP385 4.3 36.1 1.0 C A:GLY229 4.4 41.2 1.0 N A:LYS386 4.4 39.1 1.0 OE1 A:GLU230 4.4 46.6 1.0 N A:GLY388 4.5 30.5 1.0 C A:ASP385 4.7 40.0 1.0 CA A:LYS386 4.8 36.4 1.0 CG A:ASP726 4.9 32.7 1.0

Fluorine binding site 4 out of 4 in the Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1107 b:43.0 occ:1.00 F4 A:ALF1107 0.0 43.0 1.0 AL A:ALF1107 1.8 35.0 1.0 OD1 A:ASP385 2.1 50.8 1.0 F2 A:ALF1107 2.5 34.2 1.0 O A:HOH1219 2.5 44.8 1.0 F1 A:ALF1107 2.5 41.3 1.0 NZ A:LYS707 2.8 35.6 1.0 N A:GLY627 2.8 29.9 1.0 CA A:THR626 3.2 40.9 1.0 CG A:ASP385 3.3 43.7 1.0 C A:THR626 3.5 44.7 1.0 OG1 A:THR626 3.5 46.1 1.0 F3 A:ALF1107 3.6 39.0 1.0 CE A:LYS707 3.6 37.0 1.0 ND2 A:ASN729 3.7 28.1 1.0 O A:THR228 3.8 41.4 1.0 CB A:THR626 3.8 41.4 1.0 CA A:GLY627 3.9 25.2 1.0 O A:VAL625 4.0 36.9 1.0 OD2 A:ASP385 4.1 26.6 1.0 CB A:ASP385 4.2 36.1 1.0 N A:THR626 4.3 43.3 1.0 N A:LYS386 4.5 39.1 1.0 CA A:ASP385 4.6 22.3 1.0 C A:VAL625 4.6 44.7 1.0 OD1 A:ASP730 4.7 30.2 1.0 O A:HOH1238 4.7 31.4 1.0 C A:THR228 4.7 39.6 1.0 O A:THR626 4.7 36.4 1.0 N A:ASP628 4.7 36.1 1.0 C A:GLY627 4.8 41.3 1.0 CA A:GLY229 4.9 29.6 1.0 CG A:ASN729 4.9 28.7 1.0

K.Yamamoto, V.Dubey, K.Irie, H.Nakanishi, H.Khandelia, Y.Fujiyoshi, K.Abe. A Single K+-Binding Site in the Crystal Structure of the Gastric Proton Pump. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31436534
DOI: 10.7554/ELIFE.47701