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Fluorine in PDB 6jxk: Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)

Enzymatic activity of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)

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

Protein crystallography data

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

Resolution Low / High (Å) 47.79 / 4.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 191.510, 106.430, 250.960, 90.00, 107.79, 90.00
R / Rfree (%) 26.3 / 33.8

Other elements in 6jxk:

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

Magnesium (Mg) 4 atoms
Potassium (K) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type) (pdb code 6jxk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type), PDB code: 6jxk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6jxk

Go back to Fluorine Binding Sites List in 6jxk
Fluorine binding site 1 out of 8 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


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 (Wild-Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:0.8
occ:1.00
 F1 A:MF41101 0.0 0.8 1.0
O A:THR228 2.0 0.3 1.0
MG A:MF41101 2.0 0.1 1.0
C A:THR228 3.1 93.0 1.0
F2 A:MF41101 3.2 93.7 1.0
CG A:GLU230 3.2 0.6 1.0
F4 A:MF41101 3.2 0.8 1.0
OG1 A:THR387 3.2 0.7 1.0
C A:GLY229 3.2 0.8 1.0
F3 A:MF41101 3.4 0.0 1.0
CA A:GLY229 3.4 1.0 1.0
N A:GLU230 3.5 0.8 1.0
N A:ASP628 3.5 0.7 1.0
O A:GLY229 3.6 0.3 1.0
OG1 A:THR626 3.7 93.4 1.0
N A:GLY229 3.7 95.2 1.0
N A:GLY627 3.7 96.2 1.0
C A:GLY627 3.9 0.5 1.0
CB A:GLU230 3.9 0.0 1.0
CA A:GLY627 3.9 0.7 1.0
CD A:GLU230 4.0 0.5 1.0
OE1 A:GLU230 4.0 0.3 1.0
CA A:GLU230 4.1 0.9 1.0
ND2 A:ASN729 4.2 0.5 1.0
CB A:THR387 4.2 0.4 1.0
CA A:ASP628 4.2 0.1 1.0
CA A:THR228 4.3 94.6 1.0
CB A:ASP628 4.3 94.8 1.0
CB A:THR228 4.4 91.6 1.0
OG1 A:THR228 4.6 89.0 1.0
OD1 A:ASP385 4.6 91.5 1.0
O A:GLY627 4.8 0.9 1.0
C A:THR626 4.9 88.3 1.0
CB A:THR626 5.0 94.4 1.0
CG2 A:THR387 5.0 0.5 1.0
OE2 A:GLU230 5.0 0.1 1.0

Fluorine binding site 2 out of 8 in 6jxk

Go back to Fluorine Binding Sites List in 6jxk
Fluorine binding site 2 out of 8 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


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 (Wild-Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:93.7
occ:1.00
 F2 A:MF41101 0.0 93.7 1.0
MG A:MF41101 2.0 0.1 1.0
OD2 A:ASP385 2.3 97.0 1.0
MG A:MG1102 2.4 80.3 1.0
OD1 A:ASP385 3.0 91.5 1.0
CA A:GLY229 3.0 1.0 1.0
O A:GLY229 3.0 0.3 1.0
CG A:ASP385 3.0 0.8 1.0
F4 A:MF41101 3.2 0.8 1.0
ND2 A:ASN729 3.2 0.5 1.0
F1 A:MF41101 3.2 0.8 1.0
CB A:THR387 3.3 0.4 1.0
C A:GLY229 3.3 0.8 1.0
F3 A:MF41101 3.3 0.0 1.0
OG1 A:THR387 3.5 0.7 1.0
O A:THR387 3.8 0.8 1.0
OD1 A:ASP726 3.9 0.4 1.0
O A:THR228 3.9 0.3 1.0
OD1 A:ASN729 4.0 0.7 1.0
CG A:ASN729 4.0 0.7 1.0
CA A:THR387 4.1 0.2 1.0
N A:THR387 4.1 0.1 1.0
N A:GLY229 4.1 95.2 1.0
C A:THR387 4.3 0.1 1.0
CG2 A:THR387 4.4 0.5 1.0
OD2 A:ASP726 4.4 0.2 1.0
C A:THR228 4.5 93.0 1.0
CB A:ASP385 4.5 0.2 1.0
N A:GLU230 4.5 0.8 1.0
OD2 A:ASP730 4.6 0.3 1.0
CG A:ASP726 4.6 0.2 1.0
OD1 A:ASP730 4.8 1.0 1.0
OG1 A:THR626 5.0 93.4 1.0

Fluorine binding site 3 out of 8 in 6jxk

Go back to Fluorine Binding Sites List in 6jxk
Fluorine binding site 3 out of 8 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


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 (Wild-Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:0.0
occ:1.00
 F3 A:MF41101 0.0 0.0 1.0
MG A:MF41101 2.0 0.1 1.0
OD1 A:ASP385 2.1 91.5 1.0
OG1 A:THR626 2.2 93.4 1.0
N A:THR387 2.6 0.1 1.0
OG1 A:THR387 2.7 0.7 1.0
N A:LYS386 2.9 0.6 1.0
CB A:THR626 3.2 94.4 1.0
CB A:LYS386 3.2 0.1 1.0
CG A:ASP385 3.2 0.8 1.0
CA A:LYS386 3.3 0.1 1.0
F2 A:MF41101 3.3 93.7 1.0
F4 A:MF41101 3.4 0.8 1.0
F1 A:MF41101 3.4 0.8 1.0
C A:LYS386 3.4 0.9 1.0
CB A:THR387 3.4 0.4 1.0
CA A:THR387 3.6 0.2 1.0
OD2 A:ASP385 3.8 97.0 1.0
CA A:THR626 3.9 0.7 1.0
CE A:LYS386 4.0 0.7 1.0
C A:ASP385 4.0 0.1 1.0
N A:GLY627 4.3 96.2 1.0
CG A:LYS386 4.3 0.5 1.0
CA A:ASP385 4.4 0.1 1.0
CB A:ASP385 4.4 0.2 1.0
CG2 A:THR626 4.4 87.2 1.0
O A:THR387 4.6 0.8 1.0
O A:LYS386 4.6 0.1 1.0
C A:THR387 4.6 0.1 1.0
C A:THR626 4.6 88.3 1.0
CD A:LYS386 4.7 0.3 1.0
N A:ASP628 4.7 0.7 1.0
CB A:ASP628 4.7 94.8 1.0
OE1 A:GLU230 4.9 0.3 1.0
MG A:MG1102 4.9 80.3 1.0
CG2 A:THR387 4.9 0.5 1.0
O A:THR228 5.0 0.3 1.0
O A:VAL625 5.0 0.3 1.0

Fluorine binding site 4 out of 8 in 6jxk

Go back to Fluorine Binding Sites List in 6jxk
Fluorine binding site 4 out of 8 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


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 (Wild-Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:0.8
occ:1.00
 F4 A:MF41101 0.0 0.8 1.0
MG A:MF41101 2.0 0.1 1.0
ND2 A:ASN729 2.4 0.5 1.0
N A:GLY627 3.0 96.2 1.0
NZ A:LYS707 3.1 0.4 1.0
F2 A:MF41101 3.2 93.7 1.0
F1 A:MF41101 3.2 0.8 1.0
O A:THR228 3.3 0.3 1.0
F3 A:MF41101 3.4 0.0 1.0
OD1 A:ASP385 3.4 91.5 1.0
OD2 A:ASP385 3.4 97.0 1.0
CA A:THR626 3.5 0.7 1.0
CE A:LYS707 3.5 0.8 1.0
CG A:ASP385 3.5 0.8 1.0
C A:THR626 3.6 88.3 1.0
OG1 A:THR626 3.6 93.4 1.0
CG A:ASN729 3.7 0.7 1.0
CA A:GLY627 3.9 0.7 1.0
CB A:THR626 4.2 94.4 1.0
C A:THR228 4.2 93.0 1.0
O A:VAL625 4.3 0.3 1.0
OD1 A:ASP730 4.3 1.0 1.0
CA A:GLY229 4.4 1.0 1.0
OD1 A:ASN729 4.5 0.7 1.0
CB A:ASN729 4.5 1.0 1.0
CB A:ASP385 4.6 0.2 1.0
N A:GLY229 4.6 95.2 1.0
N A:THR626 4.6 0.7 1.0
O A:THR626 4.7 64.4 1.0
N A:ASP628 4.9 0.7 1.0
C A:VAL625 4.9 0.5 1.0
C A:GLY627 4.9 0.5 1.0
CA A:ASP385 5.0 0.1 1.0

Fluorine binding site 5 out of 8 in 6jxk

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Fluorine binding site 5 out of 8 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1101

b:0.3
occ:1.00
 F1 E:MF41101 0.0 0.3 1.0
MG E:MF41101 2.0 0.3 1.0
O E:THR228 2.1 0.2 1.0
C E:GLY627 3.1 0.9 1.0
F2 E:MF41101 3.2 0.5 1.0
F4 E:MF41101 3.2 0.8 1.0
N E:GLY627 3.3 0.9 1.0
C E:THR228 3.3 0.1 1.0
F3 E:MF41101 3.3 0.4 1.0
O E:GLY627 3.3 0.6 1.0
N E:ASP628 3.4 1.0 1.0
CA E:GLY627 3.4 0.2 1.0
OG1 E:THR626 3.6 0.8 1.0
CB E:ASP628 3.8 0.5 1.0
CG E:GLU230 3.8 1.0 1.0
CA E:ASP628 3.9 0.1 1.0
OG1 E:THR387 4.0 0.2 1.0
OE1 E:GLU230 4.1 0.7 1.0
CA E:GLY229 4.1 0.9 1.0
N E:GLY229 4.1 0.6 1.0
CA E:THR228 4.2 0.7 1.0
CD E:GLU230 4.3 0.3 1.0
CB E:THR228 4.3 0.7 1.0
C E:GLY229 4.4 0.1 1.0
C E:THR626 4.4 0.6 1.0
ND2 E:ASN729 4.4 0.1 1.0
N E:GLU230 4.5 0.9 1.0
OD1 E:ASP628 4.6 0.1 1.0
CG E:ASP628 4.6 0.9 1.0
CG2 E:THR387 4.6 0.7 1.0
OD1 E:ASP385 4.8 0.1 1.0
CB E:THR626 4.8 0.6 1.0
CA E:THR626 4.9 0.1 1.0
CB E:THR387 4.9 0.4 1.0
O E:GLY229 5.0 0.6 1.0
CB E:GLU230 5.0 0.6 1.0

Fluorine binding site 6 out of 8 in 6jxk

Go back to Fluorine Binding Sites List in 6jxk
Fluorine binding site 6 out of 8 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1101

b:0.5
occ:1.00
 F2 E:MF41101 0.0 0.5 1.0
MG E:MF41101 2.0 0.3 1.0
OG1 E:THR387 2.6 0.2 1.0
CA E:GLY229 3.0 0.9 1.0
ND2 E:ASN729 3.1 0.1 1.0
OD2 E:ASP385 3.1 0.8 1.0
O E:THR228 3.1 0.2 1.0
MG E:MG1102 3.2 0.5 1.0
F4 E:MF41101 3.2 0.8 1.0
F1 E:MF41101 3.2 0.3 1.0
OD1 E:ASN729 3.3 0.6 1.0
OD1 E:ASP385 3.3 0.1 1.0
F3 E:MF41101 3.4 0.4 1.0
CG E:ASN729 3.6 0.3 1.0
CG E:ASP385 3.6 0.2 1.0
N E:GLY229 3.7 0.6 1.0
C E:THR228 3.8 0.1 1.0
C E:GLY229 3.8 0.1 1.0
O E:GLY229 4.0 0.6 1.0
CB E:THR387 4.0 0.4 1.0
OD1 E:ASP726 4.1 0.5 1.0
OD2 E:ASP730 4.3 0.4 1.0
NZ E:LYS707 4.6 0.4 1.0
N E:THR387 4.7 0.8 1.0
CG2 E:THR387 4.7 0.7 1.0
N E:GLU230 4.8 0.9 1.0
N E:GLY627 4.9 0.9 1.0
CA E:THR387 4.9 0.6 1.0
CB E:ASN729 5.0 0.1 1.0
CB E:ASP385 5.0 0.5 1.0
O E:THR387 5.0 0.9 1.0

Fluorine binding site 7 out of 8 in 6jxk

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Fluorine binding site 7 out of 8 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1101

b:0.4
occ:1.00
 F3 E:MF41101 0.0 0.4 1.0
MG E:MF41101 2.0 0.3 1.0
OD1 E:ASP385 2.1 0.1 1.0
OG1 E:THR626 2.2 0.8 1.0
N E:LYS386 2.8 0.1 1.0
N E:THR387 2.9 0.8 1.0
OG1 E:THR387 3.1 0.2 1.0
CB E:THR626 3.3 0.6 1.0
CB E:LYS386 3.3 0.3 1.0
CG E:ASP385 3.3 0.2 1.0
F1 E:MF41101 3.3 0.3 1.0
CA E:LYS386 3.3 0.5 1.0
F2 E:MF41101 3.4 0.5 1.0
F4 E:MF41101 3.4 0.8 1.0
C E:LYS386 3.6 0.8 1.0
CA E:THR626 3.8 0.1 1.0
CB E:THR387 3.9 0.4 1.0
C E:ASP385 4.0 0.4 1.0
OD2 E:ASP385 4.0 0.8 1.0
CA E:THR387 4.0 0.6 1.0
N E:GLY627 4.1 0.9 1.0
CA E:ASP385 4.3 0.7 1.0
CG2 E:THR387 4.3 0.7 1.0
CB E:ASP385 4.4 0.5 1.0
C E:THR626 4.5 0.6 1.0
CG2 E:THR626 4.6 0.3 1.0
CG E:LYS386 4.6 0.0 1.0
MG E:MG1102 4.6 0.5 1.0
O E:LYS386 4.8 0.9 1.0
CB E:ASP628 4.9 0.5 1.0
O E:THR387 4.9 0.9 1.0
O E:THR228 4.9 0.2 1.0
C E:THR387 5.0 0.7 1.0

Fluorine binding site 8 out of 8 in 6jxk

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Fluorine binding site 8 out of 8 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1101

b:0.8
occ:1.00
 F4 E:MF41101 0.0 0.8 1.0
MG E:MF41101 2.0 0.3 1.0
N E:GLY627 2.2 0.9 1.0
NZ E:LYS707 2.7 0.4 1.0
ND2 E:ASN729 2.7 0.1 1.0
C E:THR626 3.0 0.6 1.0
CA E:THR626 3.0 0.1 1.0
F2 E:MF41101 3.2 0.5 1.0
CA E:GLY627 3.2 0.2 1.0
F1 E:MF41101 3.2 0.3 1.0
F3 E:MF41101 3.4 0.4 1.0
CE E:LYS707 3.5 0.6 1.0
OG1 E:THR626 3.6 0.8 1.0
O E:THR228 3.6 0.2 1.0
OD1 E:ASP385 3.9 0.1 1.0
CB E:THR626 3.9 0.6 1.0
CG E:ASN729 4.0 0.3 1.0
O E:THR626 4.1 0.5 1.0
N E:THR626 4.2 0.7 1.0
C E:GLY627 4.2 0.9 1.0
O E:VAL625 4.2 0.5 1.0
CG E:ASP385 4.4 0.2 1.0
OD1 E:ASN729 4.5 0.6 1.0
C E:THR228 4.5 0.1 1.0
C E:VAL625 4.6 1.0 1.0
N E:ASP628 4.6 1.0 1.0
OD2 E:ASP385 4.7 0.8 1.0
OD1 E:ASP730 4.8 0.7 1.0
O E:GLY627 4.9 0.6 1.0
CD E:LYS707 4.9 0.9 1.0

Reference:

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
Page generated: Thu Aug 1 21:44:20 2024

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