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

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

The structure of K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxh 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 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.370, 103.370, 370.010, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 25.7

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

Magnesium	(Mg)	2 atoms
Potassium	(K)	6 atoms

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

Fluorine binding site 1 out of 4 in the K+-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 K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:54.9 occ:1.00 F1 A:MF41101 0.0 54.9 1.0 MG A:MF41101 2.0 45.3 1.0 O A:THR228 2.4 36.5 1.0 OE1 A:GLU230 2.9 73.5 1.0 F4 A:MF41101 3.1 41.2 1.0 F2 A:MF41101 3.2 49.3 1.0 CG A:GLU230 3.3 43.4 1.0 F3 A:MF41101 3.4 50.4 1.0 N A:GLY627 3.4 40.2 1.0 CD A:GLU230 3.4 62.2 1.0 CA A:GLY229 3.5 38.6 1.0 C A:THR228 3.5 59.8 1.0 C A:GLY229 3.5 43.7 1.0 N A:ASP628 3.6 33.0 1.0 CA A:GLY627 3.6 32.4 1.0 C A:GLY627 3.8 51.0 1.0 O A:GLY229 3.8 62.5 1.0 OG1 A:THR626 3.9 38.5 1.0 N A:GLU230 3.9 47.8 1.0 N A:GLY229 3.9 50.2 1.0 OG1 A:THR387 4.0 66.0 1.0 CB A:THR387 4.1 55.0 1.0 CB A:ASP628 4.2 43.0 1.0 CA A:ASP628 4.3 33.4 1.0 CB A:GLU230 4.5 37.4 1.0 OD1 A:ASP385 4.6 53.2 1.0 CA A:GLU230 4.6 44.0 1.0 C A:THR626 4.6 50.7 1.0 OE2 A:GLU230 4.6 72.5 1.0 O A:GLY627 4.7 54.4 1.0 ND2 A:ASN729 4.7 39.4 1.0 CA A:THR228 4.7 61.1 1.0 CA A:THR626 5.0 40.2 1.0 CB A:THR228 5.0 57.3 1.0 CB A:THR626 5.0 47.0 1.0 MG A:MG1102 5.0 49.6 1.0

Fluorine binding site 2 out of 4 in the K+-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 K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:49.3 occ:1.00 F2 A:MF41101 0.0 49.3 1.0 MG A:MF41101 2.0 45.3 1.0 MG A:MG1102 2.1 49.6 1.0 O A:HOH1219 2.3 38.8 1.0 OD2 A:ASP385 2.4 47.3 1.0 OD1 A:ASP385 2.6 53.2 1.0 CG A:ASP385 2.8 55.2 1.0 O A:THR387 3.0 56.3 1.0 F4 A:MF41101 3.2 41.2 1.0 F1 A:MF41101 3.2 54.9 1.0 F3 A:MF41101 3.3 50.4 1.0 CB A:THR387 3.6 55.0 1.0 O A:HOH1346 3.7 61.4 1.0 O A:GLY229 3.7 62.5 1.0 CA A:GLY229 3.8 38.6 1.0 N A:THR387 3.8 49.9 1.0 C A:THR387 3.8 50.4 1.0 CA A:THR387 3.9 53.0 1.0 OD1 A:ASP726 4.0 44.5 1.0 C A:GLY229 4.1 43.7 1.0 OD1 A:ASN729 4.2 40.8 1.0 CB A:ASP385 4.3 49.6 1.0 OG1 A:THR387 4.4 66.0 1.0 OD2 A:ASP730 4.4 74.5 1.0 ND2 A:ASN729 4.5 39.4 1.0 CG2 A:THR387 4.6 46.4 1.0 O A:THR228 4.6 36.5 1.0 C A:LYS386 4.8 54.6 1.0 CG A:ASN729 4.8 45.4 1.0 NZ A:LYS707 4.8 39.3 1.0 N A:LYS386 4.8 60.7 1.0 OE1 A:GLU230 4.9 73.5 1.0 N A:GLY229 4.9 50.2 1.0

Fluorine binding site 3 out of 4 in the K+-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 K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:50.4 occ:1.00 F3 A:MF41101 0.0 50.4 1.0 MG A:MF41101 2.0 45.3 1.0 OG1 A:THR626 2.7 38.5 1.0 OD1 A:ASP385 2.7 53.2 1.0 N A:THR387 2.9 49.9 1.0 N A:LYS386 2.9 60.7 1.0 CB A:THR626 3.0 47.0 1.0 CB A:LYS386 3.2 45.4 1.0 F2 A:MF41101 3.3 49.3 1.0 F4 A:MF41101 3.3 41.2 1.0 CA A:LYS386 3.3 48.2 1.0 CA A:THR626 3.4 40.2 1.0 F1 A:MF41101 3.4 54.9 1.0 CG A:ASP385 3.5 55.2 1.0 C A:LYS386 3.6 54.6 1.0 OG1 A:THR387 3.8 66.0 1.0 N A:GLY627 3.9 40.2 1.0 CB A:THR387 3.9 55.0 1.0 CA A:THR387 4.0 53.0 1.0 OD2 A:ASP385 4.0 47.3 1.0 C A:ASP385 4.0 52.7 1.0 C A:THR626 4.2 50.7 1.0 CA A:ASP385 4.3 32.4 1.0 CE A:LYS386 4.3 51.5 1.0 CG A:LYS386 4.3 43.1 1.0 O A:VAL625 4.5 42.5 1.0 CG2 A:THR626 4.5 37.5 1.0 CB A:ASP385 4.5 49.6 1.0 N A:THR626 4.5 49.1 1.0 OE1 A:GLU230 4.5 73.5 1.0 O A:THR387 4.7 56.3 1.0 O A:LYS386 4.8 49.7 1.0 CD A:LYS386 4.8 48.9 1.0 NZ A:LYS707 4.8 39.3 1.0 N A:ASP628 4.8 33.0 1.0 C A:THR387 4.8 50.4 1.0 C A:VAL625 4.9 48.6 1.0 CB A:ASP628 4.9 43.0 1.0

Fluorine binding site 4 out of 4 in the K+-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 K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:41.2 occ:1.00 F4 A:MF41101 0.0 41.2 1.0 MG A:MF41101 2.0 45.3 1.0 NZ A:LYS707 2.4 39.3 1.0 OD1 A:ASP385 2.7 53.2 1.0 ND2 A:ASN729 2.8 39.4 1.0 N A:GLY627 2.8 40.2 1.0 F1 A:MF41101 3.1 54.9 1.0 F2 A:MF41101 3.2 49.3 1.0 F3 A:MF41101 3.3 50.4 1.0 CE A:LYS707 3.3 33.6 1.0 O A:THR228 3.5 36.5 1.0 C A:THR626 3.7 50.7 1.0 CA A:THR626 3.7 40.2 1.0 CA A:GLY627 3.7 32.4 1.0 CG A:ASP385 3.8 55.2 1.0 CG A:ASN729 3.9 45.4 1.0 OD1 A:ASN729 4.2 40.8 1.0 O A:HOH1219 4.2 38.8 1.0 OD1 A:ASP730 4.2 70.7 1.0 O A:VAL625 4.2 42.5 1.0 OG1 A:THR626 4.3 38.5 1.0 O A:HOH1277 4.4 52.3 1.0 OD2 A:ASP385 4.4 47.3 1.0 C A:THR228 4.4 59.8 1.0 CA A:GLY229 4.5 38.6 1.0 CB A:THR626 4.6 47.0 1.0 CD A:LYS707 4.7 30.9 1.0 N A:THR626 4.7 49.1 1.0 N A:GLY229 4.8 50.2 1.0 O A:THR626 4.8 39.0 1.0 C A:GLY627 4.9 51.0 1.0 OD2 A:ASP730 4.9 74.5 1.0 CB A:ASP385 4.9 49.6 1.0 CG A:ASP730 4.9 63.2 1.0 C A:VAL625 4.9 48.6 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