Fluorine in PDB 7drx: Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in 90PS with Beryllium Fluoride (E2P State)

All present enzymatic activity of Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in 90PS with Beryllium Fluoride (E2P State):
7.6.2.1;

The structure of Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in 90PS with Beryllium Fluoride (E2P State) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in 90PS with Beryllium Fluoride (E2P State) (pdb code 7drx). 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 90PS with Beryllium Fluoride (E2P State), PDB code: 7drx:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in 90PS 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 90PS with Beryllium Fluoride (E2P State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1602 b:19.6 occ:1.00 F1 A:BEF1602 0.0 19.6 1.0 BE A:BEF1602 1.8 19.6 1.0 OD2 A:ASP667 2.2 17.5 1.0 O A:THR669 2.2 19.8 1.0 OD1 A:ASP1130 2.3 18.1 1.0 O A:ASP1130 2.6 18.1 1.0 OG1 A:THR671 2.8 17.0 1.0 F2 A:BEF1602 3.0 19.6 1.0 F3 A:BEF1602 3.1 19.6 1.0 CG A:ASP667 3.2 17.5 1.0 C A:THR669 3.4 19.8 1.0 OD2 A:ASP1134 3.4 20.1 1.0 CG A:ASP1130 3.5 18.1 1.0 N A:ASP1130 3.6 18.1 1.0 N A:THR671 3.6 17.0 1.0 C A:ASP1130 3.7 18.1 1.0 CB A:ASP667 3.7 17.5 1.0 CB A:THR671 3.8 17.0 1.0 CA A:ASP1130 4.0 18.1 1.0 MG A:MG1601 4.1 18.1 1.0 C A:GLY670 4.1 18.6 1.0 N A:GLY670 4.2 18.6 1.0 CA A:GLY670 4.2 18.6 1.0 N A:THR669 4.2 19.8 1.0 OD1 A:ASP667 4.2 17.5 1.0 OD2 A:ASP1130 4.3 18.1 1.0 CA A:THR671 4.3 17.0 1.0 CA A:THR669 4.3 19.8 1.0 CB A:ASP1130 4.3 18.1 1.0 CG A:ASP1134 4.6 20.1 1.0 C A:GLY1129 4.7 13.6 1.0 C A:LYS668 4.7 20.2 1.0 CA A:GLY1129 4.8 13.6 1.0 N A:LYS668 4.8 20.2 1.0 N A:GLY1131 4.8 22.3 1.0 CB A:THR669 4.9 19.8 1.0 C A:ASP667 4.9 17.5 1.0 CA A:ASP667 4.9 17.5 1.0

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in 90PS 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 90PS with Beryllium Fluoride (E2P State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1602 b:19.6 occ:1.00 F2 A:BEF1602 0.0 19.6 1.0 BE A:BEF1602 1.8 19.6 1.0 OD1 A:ASN1133 2.3 22.6 1.0 O A:ASP1130 2.8 18.1 1.0 OD2 A:ASP1134 3.0 20.1 1.0 F1 A:BEF1602 3.0 19.6 1.0 F3 A:BEF1602 3.0 19.6 1.0 OD2 A:ASP667 3.0 17.5 1.0 CG A:ASN1133 3.1 22.6 1.0 ND2 A:ASN1133 3.2 22.6 1.0 MG A:MG1601 3.4 18.1 1.0 CG A:ASP667 3.6 17.5 1.0 CG A:ASP1134 3.6 20.1 1.0 OD1 A:ASP667 3.7 17.5 1.0 O A:ASP439 3.8 31.4 1.0 OD1 A:ASP1134 3.9 20.1 1.0 C A:ASP1130 3.9 18.1 1.0 CA A:GLY1131 3.9 22.3 1.0 O A:LYS436 4.0 30.0 1.0 O A:THR669 4.2 19.8 1.0 NZ A:LYS1110 4.4 20.4 1.0 N A:GLY1131 4.5 22.3 1.0 C A:GLY1131 4.5 22.3 1.0 C A:ASP439 4.6 31.4 1.0 CB A:ASN1133 4.6 22.6 1.0 CB A:ASP667 4.7 17.5 1.0 CB A:ASP1134 4.7 20.1 1.0 OD1 A:ASP1130 4.8 18.1 1.0 O A:GLY1131 4.8 22.3 1.0 N A:ASP1134 4.8 20.1 1.0 O A:ASN437 4.9 29.6 1.0 N A:ASN1133 4.9 22.6 1.0

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in 90PS 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 90PS with Beryllium Fluoride (E2P State) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1602 b:19.6 occ:1.00 F3 A:BEF1602 0.0 19.6 1.0 BE A:BEF1602 1.8 19.6 1.0 O A:THR669 2.3 19.8 1.0 O A:LYS436 2.6 30.0 1.0 F2 A:BEF1602 3.0 19.6 1.0 F1 A:BEF1602 3.1 19.6 1.0 C A:THR669 3.2 19.8 1.0 CB A:THR669 3.5 19.8 1.0 O A:ASP439 3.5 31.4 1.0 CG2 A:THR669 3.5 19.8 1.0 C A:LYS436 3.8 30.0 1.0 OD2 A:ASP667 3.8 17.5 1.0 CA A:THR669 3.9 19.8 1.0 O A:ASP1130 3.9 18.1 1.0 MG A:MG1601 4.1 18.1 1.0 N A:GLY670 4.1 18.6 1.0 CB A:LYS436 4.2 30.0 1.0 CA A:LYS436 4.3 30.0 1.0 CA A:GLY440 4.3 29.8 1.0 OD1 A:ASP1130 4.4 18.1 1.0 N A:THR669 4.5 19.8 1.0 CA A:GLY670 4.5 18.6 1.0 C A:ASP439 4.6 31.4 1.0 CG A:LYS436 4.7 30.0 1.0 OG1 A:THR669 4.7 19.8 1.0 N A:ASN437 4.9 29.6 1.0 N A:GLY440 4.9 29.8 1.0 CG A:ASP667 5.0 17.5 1.0 C A:ASP1130 5.0 18.1 1.0

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