Fluorine in PDB 7whv: Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State)

Enzymatic activity of Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State)

All present enzymatic activity of Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State):
7.6.2.1;

Other elements in 7whv:

The structure of Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State) 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 DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State) (pdb code 7whv). 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 DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State), PDB code: 7whv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7whv

Go back to Fluorine Binding Sites List in 7whv
Fluorine binding site 1 out of 3 in the Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State)


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 DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1602

b:26.5
occ:1.00
 F1 A:BEF1602 0.0 26.5 1.0
BE A:BEF1602 1.7 26.5 1.0
OD2 A:ASP667 2.1 23.9 1.0
OD1 A:ASP1130 2.1 25.2 1.0
O A:THR669 2.2 26.0 1.0
OG1 A:THR671 2.8 23.7 1.0
O A:ASP1130 2.8 25.2 1.0
F2 A:BEF1602 3.0 26.5 1.0
F3 A:BEF1602 3.0 26.5 1.0
CG A:ASP667 3.1 23.9 1.0
C A:THR669 3.2 26.0 1.0
CG A:ASP1130 3.2 25.2 1.0
N A:THR671 3.3 23.7 1.0
CB A:THR671 3.6 23.7 1.0
OD2 A:ASP1134 3.6 25.2 1.0
CB A:ASP667 3.7 23.9 1.0
N A:ASP1130 3.7 25.2 1.0
C A:ASP1130 3.8 25.2 1.0
OD2 A:ASP1130 3.8 25.2 1.0
C A:GLY670 3.9 25.6 1.0
N A:GLY670 4.0 25.6 1.0
CA A:GLY670 4.0 25.6 1.0
N A:THR669 4.0 26.0 1.0
CA A:THR671 4.0 23.7 1.0
OD1 A:ASP667 4.1 23.9 1.0
CA A:THR669 4.1 26.0 1.0
MG A:MG1601 4.1 24.9 1.0
CA A:ASP1130 4.2 25.2 1.0
CB A:ASP1130 4.3 25.2 1.0
C A:LYS668 4.4 26.5 1.0
O A:LYS668 4.7 26.5 1.0
CB A:THR669 4.7 26.0 1.0
CG A:ASP1134 4.8 25.2 1.0
O A:GLY670 4.8 25.6 1.0
N A:LYS668 4.8 26.5 1.0
C A:GLY1129 4.8 21.3 1.0
C A:ASP667 4.8 23.9 1.0
CA A:ASP667 4.9 23.9 1.0
CG2 A:THR671 4.9 23.7 1.0
CA A:GLY1129 5.0 21.3 1.0
N A:GLY1131 5.0 25.8 1.0

Fluorine binding site 2 out of 3 in 7whv

Go back to Fluorine Binding Sites List in 7whv
Fluorine binding site 2 out of 3 in the Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State)


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 DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1602

b:26.5
occ:1.00
 F2 A:BEF1602 0.0 26.5 1.0
BE A:BEF1602 1.8 26.5 1.0
OD1 A:ASN1133 2.3 25.8 1.0
O A:ASP1130 2.5 25.2 1.0
OD2 A:ASP1134 2.8 25.2 1.0
F1 A:BEF1602 3.0 26.5 1.0
F3 A:BEF1602 3.1 26.5 1.0
CG A:ASN1133 3.1 25.8 1.0
OD2 A:ASP667 3.1 23.9 1.0
ND2 A:ASN1133 3.2 25.8 1.0
CG A:ASP667 3.5 23.9 1.0
CG A:ASP1134 3.6 25.2 1.0
OD1 A:ASP667 3.6 23.9 1.0
MG A:MG1601 3.6 24.9 1.0
C A:ASP1130 3.7 25.2 1.0
O A:LYS436 3.8 30.9 1.0
CA A:GLY1131 3.9 25.8 1.0
O A:ASP439 4.0 32.7 1.0
OD1 A:ASP1134 4.0 25.2 1.0
O A:THR669 4.2 26.0 1.0
N A:GLY1131 4.3 25.8 1.0
C A:GLY1131 4.3 25.8 1.0
NZ A:LYS1110 4.4 25.9 1.0
OD1 A:ASP1130 4.4 25.2 1.0
CB A:ASP667 4.4 23.9 1.0
CB A:ASN1133 4.5 25.8 1.0
N A:ASP1134 4.5 25.2 1.0
CB A:ASP1134 4.6 25.2 1.0
O A:ASN437 4.6 31.4 1.0
O A:GLY1131 4.7 25.8 1.0
N A:ASP1130 4.7 25.2 1.0
N A:ASN1133 4.8 25.8 1.0
C A:ASP439 4.8 32.7 1.0
CA A:ASP1130 4.8 25.2 1.0
N A:SER1132 4.8 27.4 1.0

Fluorine binding site 3 out of 3 in 7whv

Go back to Fluorine Binding Sites List in 7whv
Fluorine binding site 3 out of 3 in the Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State)


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 DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1602

b:26.5
occ:1.00
 F3 A:BEF1602 0.0 26.5 1.0
BE A:BEF1602 1.8 26.5 1.0
O A:THR669 2.4 26.0 1.0
O A:LYS436 2.4 30.9 1.0
F1 A:BEF1602 3.0 26.5 1.0
F2 A:BEF1602 3.1 26.5 1.0
C A:THR669 3.5 26.0 1.0
C A:LYS436 3.5 30.9 1.0
O A:ASP439 3.5 32.7 1.0
CB A:LYS436 3.7 30.9 1.0
CB A:THR669 3.8 26.0 1.0
CG2 A:THR669 3.8 26.0 1.0
O A:ASP1130 3.9 25.2 1.0
CA A:LYS436 3.9 30.9 1.0
OD2 A:ASP667 3.9 23.9 1.0
CE A:LYS436 4.0 30.9 1.0
OD1 A:ASP1130 4.2 25.2 1.0
CA A:THR669 4.2 26.0 1.0
CA A:GLY440 4.2 31.6 1.0
MG A:MG1601 4.2 24.9 1.0
N A:GLY670 4.4 25.6 1.0
NZ A:LYS436 4.5 30.9 1.0
CA A:GLY670 4.5 25.6 1.0
OD2 A:ASP1130 4.6 25.2 1.0
CG A:LYS436 4.6 30.9 1.0
C A:ASP439 4.6 32.7 1.0
N A:ASN437 4.6 31.4 1.0
CG A:ASP1130 4.6 25.2 1.0
N A:THR669 4.8 26.0 1.0
C A:ASP1130 4.8 25.2 1.0
CD A:LYS436 4.9 30.9 1.0
OD1 A:ASN1133 4.9 25.8 1.0
N A:GLY440 4.9 31.6 1.0
CG A:ASP667 5.0 23.9 1.0

Reference:

J.Xu, Y.He, X.Wu, L.Li. Conformational Changes of A Phosphatidylcholine Flippase in Lipid Membranes. Cell Rep V. 38 10518 2022.
ISSN: ESSN 2211-1247
PubMed: 35294892
DOI: 10.1016/J.CELREP.2022.110518
Page generated: Wed Apr 5 01:41:30 2023

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