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

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

The structure of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxi 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)	47.67 / 2.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.380, 103.380, 369.860, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 26.3

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

Rubidium	(Rb)	6 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Fluorine atom in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) (pdb code 6jxi). 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-Mgf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxi:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Rb+-Bound E2-Mgf 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-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:59.6 occ:1.00 F1 A:MF41101 0.0 59.6 1.0 MG A:MF41101 2.0 35.7 1.0 O A:THR228 2.3 26.6 1.0 OE1 A:GLU230 2.7 49.9 1.0 F4 A:MF41101 3.1 28.2 1.0 F2 A:MF41101 3.2 41.6 1.0 CD A:GLU230 3.3 37.5 1.0 C A:THR228 3.4 46.5 1.0 CG A:GLU230 3.4 36.7 1.0 N A:GLY627 3.4 25.8 1.0 F3 A:MF41101 3.4 33.7 1.0 N A:ASP628 3.5 26.4 1.0 CA A:GLY229 3.6 25.2 1.0 C A:GLY229 3.7 34.0 1.0 OG1 A:THR626 3.7 35.3 1.0 CA A:GLY627 3.8 27.2 1.0 N A:GLU230 3.8 26.8 1.0 C A:GLY627 3.8 41.6 1.0 OG1 A:THR387 3.9 52.5 1.0 N A:GLY229 4.0 41.5 1.0 CB A:THR387 4.1 40.1 1.0 O A:GLY229 4.2 52.6 1.0 CB A:ASP628 4.2 44.3 1.0 CA A:ASP628 4.2 30.6 1.0 OE2 A:GLU230 4.4 33.3 1.0 CB A:GLU230 4.5 26.4 1.0 C A:THR626 4.5 41.2 1.0 OD1 A:ASP385 4.5 44.8 1.0 CA A:GLU230 4.6 30.8 1.0 CA A:THR228 4.6 48.0 1.0 ND2 A:ASN729 4.6 27.2 1.0 O A:GLY627 4.7 45.3 1.0 CA A:THR626 4.8 36.5 1.0 CB A:THR626 4.8 28.4 1.0 CB A:THR228 4.8 47.8 1.0 MG A:MG1105 5.0 44.9 1.0

Fluorine binding site 2 out of 4 in the Rb+-Bound E2-Mgf 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-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:41.6 occ:1.00 F2 A:MF41101 0.0 41.6 1.0 MG A:MG1105 1.9 44.9 1.0 MG A:MF41101 2.0 35.7 1.0 O A:HOH1285 2.3 27.6 1.0 OD1 A:ASP385 2.7 44.8 1.0 OD2 A:ASP385 2.8 40.6 1.0 O A:THR387 3.0 47.7 1.0 CG A:ASP385 3.1 43.5 1.0 F4 A:MF41101 3.1 28.2 1.0 F1 A:MF41101 3.2 59.6 1.0 F3 A:MF41101 3.3 33.7 1.0 O A:HOH1273 3.4 43.1 1.0 CB A:THR387 3.5 40.1 1.0 CA A:GLY229 3.5 25.2 1.0 O A:GLY229 3.7 52.6 1.0 N A:THR387 3.8 28.5 1.0 C A:THR387 3.9 41.7 1.0 C A:GLY229 3.9 34.0 1.0 CA A:THR387 3.9 38.9 1.0 OD1 A:ASP726 4.0 49.5 1.0 OD1 A:ASN729 4.2 25.6 1.0 O A:THR228 4.2 26.6 1.0 ND2 A:ASN729 4.3 27.2 1.0 OG1 A:THR387 4.3 52.5 1.0 CG2 A:THR387 4.4 26.3 1.0 CB A:ASP385 4.6 36.8 1.0 N A:GLY229 4.6 41.5 1.0 OE1 A:GLU230 4.7 49.9 1.0 OD2 A:ASP730 4.7 51.5 1.0 CG A:ASN729 4.7 29.5 1.0 C A:THR228 4.9 46.5 1.0 NZ A:LYS707 4.9 33.7 1.0 C A:LYS386 4.9 41.4 1.0 N A:GLU230 4.9 26.8 1.0 N A:LYS386 5.0 45.4 1.0

Fluorine binding site 3 out of 4 in the Rb+-Bound E2-Mgf 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-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:33.7 occ:1.00 F3 A:MF41101 0.0 33.7 1.0 MG A:MF41101 2.0 35.7 1.0 N A:THR387 2.7 28.5 1.0 OG1 A:THR626 2.7 35.3 1.0 OD1 A:ASP385 2.7 44.8 1.0 N A:LYS386 2.8 45.4 1.0 CB A:THR626 3.1 28.4 1.0 CB A:LYS386 3.1 26.4 1.0 CA A:LYS386 3.2 40.0 1.0 F4 A:MF41101 3.3 28.2 1.0 F2 A:MF41101 3.3 41.6 1.0 CG A:ASP385 3.4 43.5 1.0 C A:LYS386 3.4 41.4 1.0 F1 A:MF41101 3.4 59.6 1.0 CA A:THR626 3.5 36.5 1.0 OG1 A:THR387 3.7 52.5 1.0 CA A:THR387 3.8 38.9 1.0 CB A:THR387 3.8 40.1 1.0 OD2 A:ASP385 3.8 40.6 1.0 C A:ASP385 3.9 40.5 1.0 N A:GLY627 4.1 25.8 1.0 CA A:ASP385 4.2 24.9 1.0 CG A:LYS386 4.2 38.1 1.0 C A:THR626 4.3 41.2 1.0 CB A:ASP385 4.4 36.8 1.0 O A:VAL625 4.4 46.3 1.0 OE1 A:GLU230 4.4 49.9 1.0 O A:THR387 4.5 47.7 1.0 CG2 A:THR626 4.6 33.7 1.0 CE A:LYS386 4.6 38.0 1.0 N A:THR626 4.6 41.8 1.0 MG A:MG1105 4.6 44.9 1.0 O A:LYS386 4.6 30.8 1.0 C A:THR387 4.6 41.7 1.0 NZ A:LYS707 4.8 33.7 1.0 CD A:LYS386 4.9 33.6 1.0 C A:VAL625 4.9 46.5 1.0 O A:ASP385 5.0 32.8 1.0 N A:ASP628 5.0 26.4 1.0

Fluorine binding site 4 out of 4 in the Rb+-Bound E2-Mgf 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-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:28.2 occ:1.00 F4 A:MF41101 0.0 28.2 1.0 MG A:MF41101 2.0 35.7 1.0 OD1 A:ASP385 2.5 44.8 1.0 NZ A:LYS707 2.5 33.7 1.0 ND2 A:ASN729 2.7 27.2 1.0 N A:GLY627 3.1 25.8 1.0 F2 A:MF41101 3.1 41.6 1.0 F1 A:MF41101 3.1 59.6 1.0 F3 A:MF41101 3.3 33.7 1.0 CE A:LYS707 3.3 27.2 1.0 O A:THR228 3.5 26.6 1.0 CG A:ASP385 3.7 43.5 1.0 CA A:THR626 3.7 36.5 1.0 C A:THR626 3.8 41.2 1.0 CG A:ASN729 3.8 29.5 1.0 O A:HOH1285 3.9 27.6 1.0 CA A:GLY627 4.0 27.2 1.0 O A:VAL625 4.1 46.3 1.0 OD1 A:ASN729 4.2 25.6 1.0 OD1 A:ASP730 4.2 33.4 1.0 OG1 A:THR626 4.3 35.3 1.0 C A:THR228 4.4 46.5 1.0 OD2 A:ASP385 4.4 40.6 1.0 O A:HOH1274 4.4 42.4 1.0 CB A:THR626 4.5 28.4 1.0 CA A:GLY229 4.6 25.2 1.0 CB A:ASP385 4.7 36.8 1.0 N A:THR626 4.7 41.8 1.0 CD A:LYS707 4.7 32.5 1.0 N A:GLY229 4.8 41.5 1.0 MG A:MG1105 4.8 44.9 1.0 C A:VAL625 4.8 46.5 1.0 O A:THR626 5.0 35.0 1.0 CG A:ASP730 5.0 45.6 1.0 OD2 A:ASP730 5.0 51.5 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