Fluorine in PDB 8ijv: Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02

Other elements in 8ijv:

The structure of Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
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-02 (pdb code 8ijv). 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-02, PDB code: 8ijv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8ijv

Go back to Fluorine Binding Sites List in 8ijv
Fluorine binding site 1 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02


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-02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:39.3
occ:1.00
 F1 A:BFD385 0.0 39.3 1.0
BE A:BFD385 1.8 23.0 1.0
OG1 A:THR626 2.2 37.4 1.0
F3 A:BFD385 2.6 35.1 1.0
N A:THR387 2.7 22.8 1.0
OD1 A:BFD385 3.0 38.1 1.0
F2 A:BFD385 3.0 44.8 1.0
OG1 A:THR387 3.1 36.6 1.0
CB A:THR626 3.1 34.0 1.0
N A:LYS386 3.2 27.3 1.0
CB A:LYS386 3.3 18.2 1.0
CB A:THR387 3.4 28.9 1.0
CA A:LYS386 3.5 32.5 1.0
C A:LYS386 3.5 24.2 1.0
CA A:THR387 3.6 21.0 1.0
CA A:THR626 3.6 26.4 1.0
CG A:BFD385 3.8 24.9 1.0
O A:GLY229 3.9 42.4 1.0
CA A:GLY229 3.9 39.2 1.0
OD2 A:BFD385 4.0 30.5 1.0
N A:GLY627 4.0 27.2 1.0
C A:THR626 4.4 28.0 1.0
C A:BFD385 4.4 23.7 1.0
MG A:MG1102 4.4 34.1 1.0
C A:GLY229 4.4 34.4 1.0
O A:THR387 4.4 41.4 1.0
CG A:LYS386 4.4 24.8 1.0
NZ A:LYS386 4.4 35.5 1.0
CG2 A:THR626 4.5 17.3 1.0
C A:THR387 4.5 24.2 1.0
CE A:LYS386 4.5 27.2 1.0
N A:ASP628 4.6 33.2 1.0
O A:VAL625 4.7 41.8 1.0
O A:LYS386 4.7 25.5 1.0
CB A:ASP628 4.8 38.0 1.0
CA A:BFD385 4.8 23.4 1.0
N A:THR626 4.8 26.3 1.0
CG2 A:THR387 4.9 23.7 1.0
NZ A:LYS707 4.9 27.8 1.0
CB A:BFD385 4.9 20.3 1.0

Fluorine binding site 2 out of 3 in 8ijv

Go back to Fluorine Binding Sites List in 8ijv
Fluorine binding site 2 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02


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-02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:44.8
occ:1.00
 F2 A:BFD385 0.0 44.8 1.0
BE A:BFD385 1.8 23.0 1.0
MG A:MG1102 2.1 34.1 1.0
F3 A:BFD385 2.6 35.1 1.0
O A:HOH1204 2.8 31.8 1.0
OD1 A:BFD385 3.0 38.1 1.0
F1 A:BFD385 3.0 39.3 1.0
O A:HOH1212 3.1 30.1 1.0
O A:THR387 3.2 41.4 1.0
CB A:THR387 3.3 28.9 1.0
CA A:GLY229 3.3 39.2 1.0
OD2 A:BFD385 3.5 30.5 1.0
O A:THR228 3.6 48.2 1.0
O A:SER225 3.6 48.7 1.0
CG A:BFD385 3.7 24.9 1.0
ND2 A:ASN729 3.8 25.6 1.0
N A:THR387 3.9 22.8 1.0
CA A:THR387 3.9 21.0 1.0
OG1 A:THR387 3.9 36.6 1.0
C A:THR387 4.0 24.2 1.0
C A:GLY229 4.1 34.4 1.0
O A:GLY229 4.2 42.4 1.0
CG2 A:THR387 4.2 23.7 1.0
N A:GLY229 4.2 41.7 1.0
C A:THR228 4.3 41.4 1.0
OD1 A:ASN729 4.3 43.0 1.0
OD1 A:ASP726 4.5 38.4 1.0
CG A:ASN729 4.5 30.1 1.0
C A:SER225 4.8 40.9 1.0
OG1 A:THR626 4.9 37.4 1.0
C A:LYS386 5.0 24.2 1.0

Fluorine binding site 3 out of 3 in 8ijv

Go back to Fluorine Binding Sites List in 8ijv
Fluorine binding site 3 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02


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-02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:35.1
occ:1.00
 F3 A:BFD385 0.0 35.1 1.0
BE A:BFD385 1.8 23.0 1.0
OD1 A:BFD385 2.6 38.1 1.0
F1 A:BFD385 2.6 39.3 1.0
F2 A:BFD385 2.6 44.8 1.0
N A:GLY627 2.9 27.2 1.0
ND2 A:ASN729 3.0 25.6 1.0
NZ A:LYS707 3.1 27.8 1.0
CA A:GLY229 3.1 39.2 1.0
OG1 A:THR626 3.5 37.4 1.0
CA A:THR626 3.6 26.4 1.0
C A:THR626 3.7 28.0 1.0
N A:GLY229 3.8 41.7 1.0
CA A:GLY627 3.8 20.2 1.0
CG A:BFD385 4.0 24.9 1.0
CE A:LYS707 4.0 36.4 1.0
CB A:THR626 4.1 34.0 1.0
O A:HOH1212 4.2 30.1 1.0
CG A:ASN729 4.2 30.1 1.0
O A:THR228 4.4 48.2 1.0
C A:THR228 4.4 41.4 1.0
MG A:MG1102 4.4 34.1 1.0
C A:GLY229 4.4 34.4 1.0
O A:VAL625 4.5 41.8 1.0
OD1 A:ASN729 4.5 43.0 1.0
OD2 A:BFD385 4.5 30.5 1.0
N A:ASP628 4.6 33.2 1.0
O A:HOH1257 4.6 40.0 1.0
O A:GLY229 4.6 42.4 1.0
C A:GLY627 4.7 26.8 1.0
N A:THR626 4.8 26.3 1.0
OD1 A:ASP730 4.8 46.1 1.0
O A:THR626 4.9 29.5 1.0
N A:THR387 4.9 22.8 1.0
N A:LYS386 4.9 27.3 1.0
OG1 A:THR387 5.0 36.6 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 20:43:52 2024

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