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Fluorine in PDB 3din: Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase

Protein crystallography data

The structure of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase, PDB code: 3din was solved by J.Zimmer, Y.Nam, T.A.Rapoport, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 4.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.616, 156.003, 358.155, 90.00, 90.00, 90.00
R / Rfree (%) 27.9 / 30.3

Other elements in 3din:

The structure of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase (pdb code 3din). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase, PDB code: 3din:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3din

Go back to Fluorine Binding Sites List in 3din
Fluorine binding site 1 out of 6 in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F874

b:0.8
occ:1.00
 F1 A:BEF874 0.0 0.8 1.0
BE A:BEF874 1.5 0.1 1.0
F2 A:BEF874 2.4 0.4 1.0
F3 A:BEF874 2.5 0.2 1.0
O2B A:ADP873 2.5 0.4 1.0
N A:THR536 2.9 0.3 1.0
NH1 A:ARG131 3.0 0.6 1.0
C A:GLY535 3.2 0.4 1.0
CA A:GLY535 3.2 0.4 1.0
OE2 A:GLU253 3.5 0.6 1.0
CA A:THR536 3.8 0.3 1.0
PB A:ADP873 3.8 0.5 1.0
O A:GLY535 4.0 0.4 1.0
C A:THR536 4.1 0.3 1.0
CZ A:ARG131 4.1 0.6 1.0
O1B A:ADP873 4.2 0.5 1.0
MG A:MG872 4.2 0.7 1.0
NZ A:LYS101 4.2 0.0 1.0
NH2 A:ARG570 4.3 0.7 1.0
OE1 A:GLU253 4.3 0.6 1.0
CD A:GLU253 4.3 0.6 1.0
NH2 A:ARG131 4.4 0.6 1.0
O A:THR536 4.4 0.3 1.0
N A:ASP537 4.5 0.0 1.0
OD1 A:ASP252 4.6 0.3 1.0
O2A A:ADP873 4.6 0.1 1.0
N A:GLY535 4.7 0.4 1.0
NE A:ARG573 4.8 0.9 1.0
O3B A:ADP873 4.8 0.5 1.0
O3A A:ADP873 4.9 0.8 1.0
CE A:LYS101 5.0 0.0 1.0
NH2 A:ARG573 5.0 0.9 1.0

Fluorine binding site 2 out of 6 in 3din

Go back to Fluorine Binding Sites List in 3din
Fluorine binding site 2 out of 6 in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F874

b:0.4
occ:1.00
 F2 A:BEF874 0.0 0.4 1.0
BE A:BEF874 1.5 0.1 1.0
NZ A:LYS101 2.3 0.0 1.0
F1 A:BEF874 2.4 0.8 1.0
F3 A:BEF874 2.5 0.2 1.0
O2B A:ADP873 2.5 0.4 1.0
CE A:LYS101 2.6 0.0 1.0
OE2 A:GLU253 2.7 0.6 1.0
MG A:MG872 3.3 0.7 1.0
OD1 A:ASP252 3.5 0.3 1.0
CD A:LYS101 3.5 0.0 1.0
CG A:LYS101 3.6 0.0 1.0
CD A:GLU253 3.7 0.6 1.0
CB A:LYS101 3.7 0.0 1.0
PB A:ADP873 4.0 0.5 1.0
OE1 A:GLU253 4.1 0.6 1.0
NH1 A:ARG131 4.2 0.6 1.0
NH2 A:ARG131 4.3 0.6 1.0
OG1 A:THR416 4.3 0.9 1.0
CG A:ASP252 4.4 0.3 1.0
O3B A:ADP873 4.5 0.5 1.0
OD2 A:ASP252 4.7 0.3 1.0
CA A:GLY535 4.7 0.4 1.0
CZ A:ARG131 4.7 0.6 1.0
O3A A:ADP873 4.7 0.8 1.0
CG A:GLU253 4.9 0.6 1.0
N A:GLU253 5.0 0.0 1.0

Fluorine binding site 3 out of 6 in 3din

Go back to Fluorine Binding Sites List in 3din
Fluorine binding site 3 out of 6 in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F874

b:0.2
occ:1.00
 F3 A:BEF874 0.0 0.2 1.0
BE A:BEF874 1.5 0.1 1.0
MG A:MG872 2.0 0.7 1.0
NH2 A:ARG131 2.2 0.6 1.0
NH1 A:ARG131 2.3 0.6 1.0
F1 A:BEF874 2.5 0.8 1.0
F2 A:BEF874 2.5 0.4 1.0
CZ A:ARG131 2.5 0.6 1.0
O2B A:ADP873 2.9 0.4 1.0
OD1 A:ASP252 3.4 0.3 1.0
NE A:ARG131 3.7 0.6 1.0
CB A:LYS101 3.8 0.0 1.0
O2A A:ADP873 3.8 0.1 1.0
OD2 A:ASP252 3.8 0.3 1.0
CG A:ASP252 4.0 0.3 1.0
PB A:ADP873 4.3 0.5 1.0
OE2 A:GLU253 4.4 0.6 1.0
CG2 A:THR102 4.4 0.4 1.0
NZ A:LYS101 4.5 0.0 1.0
OD1 A:ASP132 4.5 0.4 1.0
CG A:LYS101 4.6 0.0 1.0
O3A A:ADP873 4.6 0.8 1.0
CD A:ARG131 4.7 0.6 1.0
N A:THR102 4.7 0.8 1.0
PA A:ADP873 4.7 0.8 1.0
CE A:LYS101 4.7 0.0 1.0
C A:LYS101 4.9 0.6 1.0
OD2 A:ASP132 4.9 0.4 1.0
CD A:LYS101 5.0 0.0 1.0
O1B A:ADP873 5.0 0.5 1.0
CA A:LYS101 5.0 0.6 1.0

Fluorine binding site 4 out of 6 in 3din

Go back to Fluorine Binding Sites List in 3din
Fluorine binding site 4 out of 6 in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F874

b:0.8
occ:1.00
 F1 B:BEF874 0.0 0.8 1.0
BE B:BEF874 1.5 0.1 1.0
F2 B:BEF874 2.4 0.4 1.0
F3 B:BEF874 2.5 0.2 1.0
O2B B:ADP873 2.5 0.4 1.0
N B:THR536 3.0 0.3 1.0
NH1 B:ARG131 3.0 0.6 1.0
CA B:GLY535 3.2 0.4 1.0
C B:GLY535 3.2 0.4 1.0
OE2 B:GLU253 3.3 0.6 1.0
PB B:ADP873 3.8 0.5 1.0
CA B:THR536 3.9 0.3 1.0
O B:GLY535 4.0 0.4 1.0
CZ B:ARG131 4.1 0.6 1.0
O1B B:ADP873 4.2 0.5 1.0
CD B:GLU253 4.2 0.6 1.0
OE1 B:GLU253 4.2 0.6 1.0
C B:THR536 4.2 0.3 1.0
MG B:MG872 4.2 0.7 1.0
NH2 B:ARG570 4.3 0.7 1.0
NH2 B:ARG131 4.3 0.6 1.0
NZ B:LYS101 4.4 0.0 1.0
OD1 B:ASP252 4.5 0.3 1.0
CE B:LYS101 4.5 0.0 1.0
O B:THR536 4.5 0.3 1.0
O2A B:ADP873 4.6 0.1 1.0
N B:GLY535 4.6 0.4 1.0
N B:ASP537 4.7 0.0 1.0
O3B B:ADP873 4.8 0.5 1.0
NE B:ARG573 4.9 0.9 1.0
O3A B:ADP873 4.9 0.8 1.0

Fluorine binding site 5 out of 6 in 3din

Go back to Fluorine Binding Sites List in 3din
Fluorine binding site 5 out of 6 in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F874

b:0.4
occ:1.00
 F2 B:BEF874 0.0 0.4 1.0
BE B:BEF874 1.5 0.1 1.0
CE B:LYS101 2.1 0.0 1.0
F1 B:BEF874 2.4 0.8 1.0
NZ B:LYS101 2.5 0.0 1.0
F3 B:BEF874 2.5 0.2 1.0
O2B B:ADP873 2.5 0.4 1.0
OE2 B:GLU253 2.6 0.6 1.0
CD B:LYS101 3.1 0.0 1.0
MG B:MG872 3.3 0.7 1.0
OD1 B:ASP252 3.4 0.3 1.0
CD B:GLU253 3.6 0.6 1.0
CG B:LYS101 3.7 0.0 1.0
CB B:LYS101 3.8 0.0 1.0
PB B:ADP873 4.0 0.5 1.0
OE1 B:GLU253 4.1 0.6 1.0
OG1 B:THR416 4.2 0.9 1.0
NH1 B:ARG131 4.2 0.6 1.0
CG B:ASP252 4.3 0.3 1.0
NH2 B:ARG131 4.4 0.6 1.0
O3B B:ADP873 4.5 0.5 1.0
OD2 B:ASP252 4.6 0.3 1.0
CA B:GLY535 4.7 0.4 1.0
O3A B:ADP873 4.7 0.8 1.0
CG B:GLU253 4.8 0.6 1.0
CZ B:ARG131 4.8 0.6 1.0
N B:GLU253 4.8 0.0 1.0
CB B:GLU253 4.9 0.6 1.0

Fluorine binding site 6 out of 6 in 3din

Go back to Fluorine Binding Sites List in 3din
Fluorine binding site 6 out of 6 in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F874

b:0.2
occ:1.00
 F3 B:BEF874 0.0 0.2 1.0
BE B:BEF874 1.5 0.1 1.0
MG B:MG872 2.0 0.7 1.0
NH2 B:ARG131 2.2 0.6 1.0
NH1 B:ARG131 2.3 0.6 1.0
F1 B:BEF874 2.5 0.8 1.0
F2 B:BEF874 2.5 0.4 1.0
CZ B:ARG131 2.5 0.6 1.0
O2B B:ADP873 2.9 0.4 1.0
OD1 B:ASP252 3.3 0.3 1.0
OD2 B:ASP252 3.7 0.3 1.0
CB B:LYS101 3.8 0.0 1.0
NE B:ARG131 3.8 0.6 1.0
O2A B:ADP873 3.8 0.1 1.0
CG B:ASP252 3.9 0.3 1.0
CE B:LYS101 4.2 0.0 1.0
OE2 B:GLU253 4.3 0.6 1.0
PB B:ADP873 4.3 0.5 1.0
CD B:LYS101 4.4 0.0 1.0
CG2 B:THR102 4.5 0.4 1.0
CG B:LYS101 4.6 0.0 1.0
OD1 B:ASP132 4.6 0.4 1.0
O3A B:ADP873 4.6 0.8 1.0
NZ B:LYS101 4.6 0.0 1.0
PA B:ADP873 4.7 0.8 1.0
N B:THR102 4.7 0.8 1.0
CD B:ARG131 4.8 0.6 1.0
C B:LYS101 4.9 0.6 1.0
OD2 B:ASP132 4.9 0.4 1.0
CA B:LYS101 5.0 0.6 1.0
O1B B:ADP873 5.0 0.5 1.0

Reference:

J.Zimmer, Y.Nam, T.A.Rapoport. Structure of A Complex of the Atpase Seca and the Protein-Translocation Channel. Nature V. 455 936 2008.
ISSN: ISSN 0028-0836
PubMed: 18923516
DOI: 10.1038/NATURE07335
Page generated: Sun Dec 13 11:44:52 2020

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