Fluorine in PDB 5eul: Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate

The structure of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate, PDB code: 5eul was solved by L.Li, E.Park, J.Ling, J.Ingram, H.Ploegh, T.A.Rapoport, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.85 / 3.70
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	127.798, 127.798, 554.772, 90.00, 90.00, 120.00
R / Rfree (%)	29.5 / 31.5

The structure of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Bromine	(Br)	216 atoms
Tantalum	(Ta)	108 atoms

The binding sites of Fluorine atom in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate (pdb code 5eul). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate, PDB code: 5eul:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:0.6 occ:1.00 F1 A:BEF1002 0.0 0.6 1.0 BE A:BEF1002 1.8 0.4 1.0 O1B A:ADP1003 2.4 0.2 1.0 O3B A:ADP1003 2.7 0.7 1.0 PB A:ADP1003 3.0 0.7 1.0 F3 A:BEF1002 3.0 0.6 1.0 F2 A:BEF1002 3.0 0.3 1.0 CG2 A:THR102 3.6 0.7 1.0 CB A:THR102 3.7 0.6 1.0 N A:GLY103 3.9 0.1 1.0 O2B A:ADP1003 4.0 0.9 1.0 CA A:THR102 4.1 0.9 1.0 O A:GLY524 4.1 0.3 1.0 O3A A:ADP1003 4.2 0.0 1.0 NZ A:LYS106 4.5 0.9 1.0 C A:THR102 4.5 0.1 1.0 MG A:MG1001 4.6 0.9 1.0 C A:GLY524 4.8 0.7 1.0 CA A:GLY103 4.9 0.8 1.0

Fluorine binding site 2 out of 3 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:0.3 occ:1.00 F2 A:BEF1002 0.0 0.3 1.0 BE A:BEF1002 1.8 0.4 1.0 O1B A:ADP1003 2.3 0.2 1.0 F3 A:BEF1002 3.0 0.6 1.0 F1 A:BEF1002 3.0 0.6 1.0 CA A:GLY103 3.4 0.8 1.0 N A:GLY103 3.5 0.1 1.0 PB A:ADP1003 3.8 0.7 1.0 OD1 A:ASP492 3.9 0.6 1.0 O A:GLY524 4.2 0.3 1.0 O5' A:ADP1003 4.4 0.3 1.0 O3A A:ADP1003 4.5 0.0 1.0 C A:THR102 4.5 0.1 1.0 CB A:ASP492 4.6 0.5 1.0 O3B A:ADP1003 4.6 0.7 1.0 O2B A:ADP1003 4.6 0.9 1.0 C A:GLY103 4.6 0.9 1.0 C5' A:ADP1003 4.7 0.8 1.0 CG A:ASP492 4.7 0.0 1.0 CA A:ASP492 4.7 0.9 1.0 CA A:ARG528 4.9 0.7 1.0 C4' A:ADP1003 4.9 0.7 1.0

Fluorine binding site 3 out of 3 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:0.6 occ:1.00 F3 A:BEF1002 0.0 0.6 1.0 BE A:BEF1002 1.8 0.4 1.0 O1B A:ADP1003 2.3 0.2 1.0 O3A A:ADP1003 2.8 0.0 1.0 PB A:ADP1003 2.9 0.7 1.0 F2 A:BEF1002 3.0 0.3 1.0 F1 A:BEF1002 3.0 0.6 1.0 O3B A:ADP1003 3.1 0.7 1.0 CB A:ASP492 3.7 0.5 1.0 PA A:ADP1003 4.0 0.8 1.0 O5' A:ADP1003 4.0 0.3 1.0 N A:ASP492 4.1 0.7 1.0 C5' A:ADP1003 4.1 0.8 1.0 CA A:ASP492 4.1 0.9 1.0 MG A:MG1001 4.1 0.9 1.0 O2B A:ADP1003 4.3 0.9 1.0 N A:THR491 4.3 0.9 1.0 O1A A:ADP1003 4.4 0.6 1.0 OD1 A:ASP492 4.5 0.6 1.0 CG A:ASP492 4.6 0.0 1.0 C A:THR491 4.9 0.8 1.0

L.Li, E.Park, J.Ling, J.Ingram, H.Ploegh, T.A.Rapoport. Crystal Structure of A Substrate-Engaged Secy Protein-Translocation Channel. Nature V. 531 395 2016.
ISSN: ESSN 1476-4687
PubMed: 26950603
DOI: 10.1038/NATURE17163