Atomistry » Fluorine » PDB 7vsg-7wgs » 7w4a
Atomistry »
  Fluorine »
    PDB 7vsg-7wgs »
      7w4a »

Fluorine in PDB 7w4a: Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan

Enzymatic activity of Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan

All present enzymatic activity of Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan:
3.6.3.10;

Other elements in 7w4a:

The structure of Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan (pdb code 7w4a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan, PDB code: 7w4a:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7w4a

Go back to Fluorine Binding Sites List in 7w4a
Fluorine binding site 1 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:28.2
occ:1.00
F1 A:BFD385 0.0 28.2 1.0
BE A:BFD385 1.8 28.2 1.0
ND2 A:ASN729 2.4 32.4 1.0
F3 A:BFD385 2.6 28.2 1.0
NZ A:LYS707 2.7 31.1 1.0
OD1 A:BFD385 3.0 28.2 1.0
F2 A:BFD385 3.0 28.2 1.0
CA A:GLY229 3.2 41.5 1.0
N A:GLY627 3.4 37.2 1.0
CG A:ASN729 3.6 32.4 1.0
N A:GLY229 3.6 41.5 1.0
CE A:LYS707 3.6 31.1 1.0
OD1 A:ASN729 4.0 32.4 1.0
CA A:GLY627 4.1 37.2 1.0
C A:THR228 4.1 46.4 1.0
C A:THR626 4.1 32.4 1.0
CA A:THR626 4.2 32.4 1.0
CG A:BFD385 4.3 28.2 1.0
O A:THR228 4.3 46.4 1.0
OD1 A:ASP730 4.3 30.3 1.0
MG A:MG1103 4.4 26.5 1.0
OG1 A:THR626 4.5 32.4 1.0
C A:GLY229 4.6 41.5 1.0
OD2 A:BFD385 4.6 28.2 1.0
CB A:ASN729 4.7 32.4 1.0
CB A:THR626 4.9 32.4 1.0
O A:GLY229 5.0 41.5 1.0
CD A:LYS707 5.0 31.1 1.0

Fluorine binding site 2 out of 4 in 7w4a

Go back to Fluorine Binding Sites List in 7w4a
Fluorine binding site 2 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:28.2
occ:1.00
F2 A:BFD385 0.0 28.2 1.0
BE A:BFD385 1.8 28.2 1.0
MG A:MG1103 2.0 26.5 1.0
F3 A:BFD385 2.6 28.2 1.0
OD2 A:BFD385 2.8 28.2 1.0
O A:THR387 2.8 31.4 1.0
OD1 A:BFD385 3.0 28.2 1.0
F1 A:BFD385 3.0 28.2 1.0
CB A:THR387 3.3 31.4 1.0
CG A:BFD385 3.3 28.2 1.0
CA A:GLY229 3.5 41.5 1.0
C A:THR387 3.7 31.4 1.0
N A:THR387 3.7 31.4 1.0
CA A:THR387 3.7 31.4 1.0
O A:SER225 4.0 48.7 1.0
OG1 A:THR387 4.0 31.4 1.0
ND2 A:ASN729 4.2 32.4 1.0
O A:GLY229 4.3 41.5 1.0
CG2 A:THR387 4.3 31.4 1.0
O A:THR228 4.3 46.4 1.0
C A:GLY229 4.3 41.5 1.0
OD2 A:ASP726 4.6 29.9 1.0
N A:GLY229 4.6 41.5 1.0
C A:LYS386 4.7 28.3 1.0
OD1 A:ASN729 4.7 32.4 1.0
N A:LYS386 4.8 28.3 1.0
OD2 A:ASP730 4.8 30.3 1.0
OD1 A:ASP726 4.8 29.9 1.0
CB A:BFD385 4.8 28.2 1.0
C A:THR228 4.9 46.4 1.0
NZ A:LYS707 4.9 31.1 1.0
CG A:ASN729 4.9 32.4 1.0
N A:GLY388 5.0 29.4 1.0

Fluorine binding site 3 out of 4 in 7w4a

Go back to Fluorine Binding Sites List in 7w4a
Fluorine binding site 3 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:28.2
occ:1.00
F3 A:BFD385 0.0 28.2 1.0
BE A:BFD385 1.8 28.2 1.0
OG1 A:THR626 2.6 32.4 1.0
OD1 A:BFD385 2.6 28.2 1.0
F1 A:BFD385 2.6 28.2 1.0
F2 A:BFD385 2.6 28.2 1.0
CB A:THR626 3.2 32.4 1.0
CA A:THR626 3.3 32.4 1.0
N A:GLY627 3.5 37.2 1.0
N A:THR387 3.5 31.4 1.0
CA A:GLY229 3.6 41.5 1.0
CG A:BFD385 3.6 28.2 1.0
N A:LYS386 3.7 28.3 1.0
OG1 A:THR387 3.8 31.4 1.0
O A:GLY229 3.9 41.5 1.0
OD2 A:BFD385 3.9 28.2 1.0
C A:THR626 3.9 32.4 1.0
CB A:THR387 4.0 31.4 1.0
CB A:LYS386 4.1 28.3 1.0
O A:VAL625 4.1 27.3 1.0
NZ A:LYS707 4.1 31.1 1.0
CA A:LYS386 4.2 28.3 1.0
C A:GLY229 4.2 41.5 1.0
CA A:THR387 4.3 31.4 1.0
C A:LYS386 4.3 28.3 1.0
MG A:MG1103 4.3 26.5 1.0
N A:THR626 4.5 32.4 1.0
CA A:GLY627 4.6 37.2 1.0
O A:THR387 4.7 31.4 1.0
CG2 A:THR626 4.7 32.4 1.0
N A:GLY229 4.7 41.5 1.0
C A:VAL625 4.7 27.3 1.0
C A:BFD385 4.8 28.2 1.0
N A:ASP628 4.8 39.8 1.0
CB A:BFD385 4.9 28.2 1.0
ND2 A:ASN729 4.9 32.4 1.0
CA A:BFD385 4.9 28.2 1.0
C A:THR387 5.0 31.4 1.0

Fluorine binding site 4 out of 4 in 7w4a

Go back to Fluorine Binding Sites List in 7w4a
Fluorine binding site 4 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:24.4
occ:1.00
F01 A:8CK1101 0.0 24.4 1.0
C18 A:8CK1101 1.3 24.4 1.0
C19 A:8CK1101 2.4 24.4 1.0
C17 A:8CK1101 2.4 24.4 1.0
CB A:MET334 3.1 29.5 1.0
C A:MET334 3.2 29.5 1.0
CB A:ALA123 3.2 37.5 1.0
N A:ALA335 3.3 25.1 1.0
O A:MET334 3.4 29.5 1.0
C20 A:8CK1101 3.6 24.4 1.0
C16 A:8CK1101 3.6 24.4 1.0
CA A:ALA335 3.7 25.1 1.0
CA A:MET334 3.8 29.5 1.0
OD1 A:ASN138 4.1 37.8 1.0
O A:ILE119 4.1 27.6 1.0
CG2 A:ILE119 4.1 27.6 1.0
C14 A:8CK1101 4.1 24.4 1.0
O A:VAL331 4.2 37.7 1.0
CG2 A:VAL338 4.2 22.1 1.0
CB A:ALA335 4.4 25.1 1.0
CA A:CYS120 4.4 31.5 1.0
CG A:MET334 4.4 29.5 1.0
C A:ILE119 4.6 27.6 1.0
N A:CYS120 4.7 31.5 1.0
CA A:ALA123 4.7 37.5 1.0
SD A:MET334 4.7 29.5 1.0
N A:MET334 4.8 29.5 1.0
CB A:VAL338 4.8 22.1 1.0
C A:ALA335 4.9 25.1 1.0
SG A:CYS120 4.9 31.5 1.0

Reference:

S.Tanaka, M.Morita, T.Yamagishi, H.V.Madapally, K.Hayashida, H.Khandelia, C.Gerle, H.Shigematsu, A.Oshima, K.Abe. Structural Basis For Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump. J.Med.Chem. V. 65 7843 2022.
ISSN: ISSN 0022-2623
PubMed: 35604136
DOI: 10.1021/ACS.JMEDCHEM.2C00338
Page generated: Wed Jul 16 01:25:22 2025

Last articles

Mg in 4OKQ
Mg in 4OK9
Mg in 4OKE
Mg in 4OJI
Mg in 4OJU
Mg in 4OIR
Mg in 4OJJ
Mg in 4OIP
Mg in 4OIY
Mg in 4OIQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy