Fluorine in PDB 8ijw: Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06

Other elements in 8ijw:

The structure of Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06 (pdb code 8ijw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06, PDB code: 8ijw:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8ijw

Go back to Fluorine Binding Sites List in 8ijw
Fluorine binding site 1 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06


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 with Bound Dq-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:38.6
occ:1.00
 F1 A:BFD385 0.0 38.6 1.0
BE A:BFD385 1.8 19.4 1.0
MG A:MG1103 1.9 28.5 1.0
F3 A:BFD385 2.6 33.6 1.0
O A:HOH1210 2.7 28.4 1.0
O A:THR387 2.8 32.2 1.0
OD2 A:BFD385 2.9 35.3 1.0
O A:HOH1208 2.9 31.4 1.0
OD1 A:BFD385 3.0 29.6 1.0
F2 A:BFD385 3.0 42.8 1.0
CB A:THR387 3.3 24.2 1.0
CG A:BFD385 3.4 27.8 1.0
C A:THR387 3.7 22.1 1.0
CA A:GLY229 3.7 33.7 1.0
O A:SER225 3.7 43.3 1.0
N A:THR387 3.8 27.4 1.0
CA A:THR387 3.8 16.8 1.0
O A:THR228 3.9 46.1 1.0
ND2 A:ASN729 3.9 22.4 1.0
OD1 A:ASP726 4.1 30.7 1.0
OG1 A:THR387 4.2 32.5 1.0
OD1 A:ASN729 4.2 40.7 1.0
CG2 A:THR387 4.2 22.3 1.0
CG A:ASN729 4.5 28.5 1.0
C A:GLY229 4.6 36.7 1.0
O A:GLY229 4.6 40.9 1.0
N A:GLY229 4.6 37.1 1.0
C A:THR228 4.7 39.6 1.0
C A:LYS386 4.8 27.8 1.0
OG1 A:THR626 4.8 32.1 1.0
CB A:BFD385 4.8 20.6 1.0
NZ A:LYS707 4.9 35.0 1.0
OD2 A:ASP730 4.9 34.1 1.0
N A:LYS386 4.9 22.7 1.0
N A:GLY388 4.9 25.8 1.0
C A:SER225 5.0 37.7 1.0

Fluorine binding site 2 out of 3 in 8ijw

Go back to Fluorine Binding Sites List in 8ijw
Fluorine binding site 2 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06


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 with Bound Dq-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:42.8
occ:1.00
 F2 A:BFD385 0.0 42.8 1.0
BE A:BFD385 1.8 19.4 1.0
ND2 A:ASN729 2.6 22.4 1.0
F3 A:BFD385 2.6 33.6 1.0
N A:GLY627 2.6 27.7 1.0
OD1 A:BFD385 3.0 29.6 1.0
NZ A:LYS707 3.0 35.0 1.0
F1 A:BFD385 3.0 38.6 1.0
CA A:GLY229 3.1 33.7 1.0
CA A:GLY627 3.5 18.1 1.0
N A:GLY229 3.5 37.1 1.0
C A:THR626 3.6 27.2 1.0
OG1 A:THR626 3.6 32.1 1.0
CA A:THR626 3.6 27.5 1.0
CE A:LYS707 3.8 30.6 1.0
CG A:ASN729 3.8 28.5 1.0
C A:THR228 4.1 39.6 1.0
O A:THR228 4.1 46.1 1.0
O A:HOH1247 4.2 31.1 1.0
CB A:THR626 4.2 34.6 1.0
O A:HOH1208 4.3 31.4 1.0
CG A:BFD385 4.3 27.8 1.0
OD1 A:ASN729 4.4 40.7 1.0
C A:GLY627 4.4 25.6 1.0
C A:GLY229 4.4 36.7 1.0
N A:ASP628 4.5 36.3 1.0
OD2 A:BFD385 4.7 35.3 1.0
O A:THR626 4.7 29.8 1.0
MG A:MG1103 4.7 28.5 1.0
O A:VAL625 4.8 31.7 1.0
O A:GLY229 4.8 40.9 1.0
N A:THR626 4.8 20.5 1.0
CB A:ASN729 5.0 28.8 1.0

Fluorine binding site 3 out of 3 in 8ijw

Go back to Fluorine Binding Sites List in 8ijw
Fluorine binding site 3 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06


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 with Bound Dq-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:33.6
occ:1.00
 F3 A:BFD385 0.0 33.6 1.0
BE A:BFD385 1.8 19.4 1.0
OG1 A:THR626 2.3 32.1 1.0
OD1 A:BFD385 2.6 29.6 1.0
F1 A:BFD385 2.6 38.6 1.0
F2 A:BFD385 2.6 42.8 1.0
N A:THR387 2.8 27.4 1.0
CB A:THR626 3.3 34.6 1.0
OG1 A:THR387 3.3 32.5 1.0
CB A:THR387 3.4 24.2 1.0
N A:LYS386 3.4 22.7 1.0
CG A:BFD385 3.5 27.8 1.0
CA A:THR387 3.6 16.8 1.0
CA A:THR626 3.6 27.5 1.0
CA A:GLY229 3.7 33.7 1.0
OD2 A:BFD385 3.7 35.3 1.0
C A:LYS386 3.7 27.8 1.0
CB A:LYS386 3.8 16.5 1.0
CA A:LYS386 3.8 23.5 1.0
N A:GLY627 3.8 27.7 1.0
O A:GLY229 4.0 40.9 1.0
MG A:MG1103 4.1 28.5 1.0
O A:THR387 4.2 32.2 1.0
C A:THR626 4.3 27.2 1.0
C A:GLY229 4.3 36.7 1.0
C A:THR387 4.4 22.1 1.0
C A:BFD385 4.5 27.1 1.0
NZ A:LYS707 4.6 35.0 1.0
CG2 A:THR626 4.6 18.7 1.0
N A:ASP628 4.7 36.3 1.0
O A:VAL625 4.7 31.7 1.0
CG2 A:THR387 4.8 22.3 1.0
CB A:BFD385 4.8 20.6 1.0
CA A:BFD385 4.8 23.5 1.0
NZ A:LYS386 4.8 29.1 1.0
CG A:LYS386 4.8 21.8 1.0
O A:LYS386 4.9 29.4 1.0
N A:GLY229 4.9 37.1 1.0
N A:THR626 4.9 20.5 1.0
CA A:GLY627 4.9 18.1 1.0
O A:HOH1208 4.9 31.4 1.0
ND2 A:ASN729 4.9 22.4 1.0
CB A:ASP628 5.0 31.9 1.0
CE A:LYS386 5.0 27.9 1.0

Reference:

K.Abe, S.Yokoshima, A.Yoshimori. Deep Learning Driven De Novo Drug Design Based on Gastric Proton Pump Structures To Be Published.
Page generated: Fri Aug 2 20:43:53 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