Atomistry » Fluorine » PDB 6jsf-6kjv » 6jxk
Atomistry »
  Fluorine »
    PDB 6jsf-6kjv »
      6jxk »

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

Go back to Fluorine Binding Sites List in 6jxk
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

Go back to Fluorine Binding Sites List in 6jxk
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

Go back to Fluorine Binding Sites List in 6jxk
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy