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Fluorine in PDB 4fme: Espg-RAB1-ARF6 Complex

Protein crystallography data

The structure of Espg-RAB1-ARF6 Complex, PDB code: 4fme was solved by F.Shao, Y.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 4.10
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 137.222, 137.222, 126.503, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.9

Other elements in 4fme:

The structure of Espg-RAB1-ARF6 Complex also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Espg-RAB1-ARF6 Complex (pdb code 4fme). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Espg-RAB1-ARF6 Complex, PDB code: 4fme:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4fme

Go back to Fluorine Binding Sites List in 4fme
Fluorine binding site 1 out of 6 in the Espg-RAB1-ARF6 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Espg-RAB1-ARF6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:0.9
occ:1.00
 F1 B:AF3201 0.0 0.9 1.0
AL B:AF3201 1.7 0.0 1.0
O2B B:GDP202 2.5 1.0 1.0
O A:HOH401 2.6 0.8 1.0
O1B B:GDP202 2.6 0.6 1.0
PB B:GDP202 2.9 0.9 1.0
F3 B:AF3201 2.9 0.0 1.0
F2 B:AF3201 3.0 0.2 1.0
NZ B:LYS24 3.3 0.8 1.0
O3B B:GDP202 3.3 0.4 1.0
MG B:MG203 3.4 85.5 1.0
CE B:LYS24 3.6 0.8 1.0
N B:GLY69 3.7 0.4 1.0
O B:THR67 3.8 0.9 1.0
CA B:ALA68 3.9 0.2 1.0
C B:ALA68 4.0 0.2 1.0
CA B:SER20 4.1 0.9 1.0
CB B:SER20 4.4 0.4 1.0
N B:GLY21 4.4 0.7 1.0
O3A B:GDP202 4.5 0.8 1.0
CA B:GLY69 4.5 0.4 1.0
O B:HOH301 4.5 88.5 1.0
C B:THR67 4.6 0.9 1.0
N B:ALA68 4.7 0.2 1.0
O B:ALA68 4.8 0.2 1.0
CB B:LYS24 4.8 0.8 1.0
C B:SER20 4.9 0.9 1.0
O B:ASP19 4.9 0.2 1.0
NH2 A:ARG208 4.9 0.2 1.0
CD B:LYS24 4.9 0.8 1.0
CB B:ALA68 5.0 0.3 1.0

Fluorine binding site 2 out of 6 in 4fme

Go back to Fluorine Binding Sites List in 4fme
Fluorine binding site 2 out of 6 in the Espg-RAB1-ARF6 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Espg-RAB1-ARF6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:0.2
occ:1.00
 F2 B:AF3201 0.0 0.2 1.0
AL B:AF3201 1.7 0.0 1.0
O A:HOH401 2.6 0.8 1.0
O B:HOH301 2.6 88.5 1.0
O1B B:GDP202 2.6 0.6 1.0
MG B:MG203 2.8 85.5 1.0
N B:THR43 2.8 0.6 1.0
F3 B:AF3201 3.0 0.0 1.0
F1 B:AF3201 3.0 0.9 1.0
NH2 A:ARG208 3.2 0.2 1.0
CB B:THR43 3.2 0.7 1.0
CA B:THR43 3.5 0.6 1.0
O B:THR43 3.6 0.6 1.0
OG1 B:THR43 3.7 0.7 1.0
C B:SER42 3.8 0.8 1.0
PB B:GDP202 3.9 0.9 1.0
CA B:SER42 4.0 0.8 1.0
C B:THR43 4.0 0.6 1.0
CB B:SER42 4.2 0.2 1.0
O3B B:GDP202 4.3 0.4 1.0
OE1 A:GLN293 4.4 0.9 1.0
CZ A:ARG208 4.4 0.2 1.0
O2A B:GDP202 4.5 0.1 1.0
CG2 B:THR43 4.5 0.7 1.0
O2B B:GDP202 4.6 1.0 1.0
CA B:ALA68 4.7 0.2 1.0
O B:SER42 4.8 0.8 1.0
NH1 A:ARG208 4.9 0.2 1.0
OG B:SER25 4.9 1.0 1.0

Fluorine binding site 3 out of 6 in 4fme

Go back to Fluorine Binding Sites List in 4fme
Fluorine binding site 3 out of 6 in the Espg-RAB1-ARF6 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Espg-RAB1-ARF6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:0.0
occ:1.00
 F3 B:AF3201 0.0 0.0 1.0
AL B:AF3201 1.7 0.0 1.0
O A:HOH401 2.6 0.8 1.0
O1B B:GDP202 2.6 0.6 1.0
NH2 A:ARG208 2.7 0.2 1.0
NH1 A:ARG208 2.8 0.2 1.0
F1 B:AF3201 2.9 0.9 1.0
F2 B:AF3201 3.0 0.2 1.0
CZ A:ARG208 3.1 0.2 1.0
CB B:SER20 3.3 0.4 1.0
N B:GLY21 3.3 0.7 1.0
CA B:SER20 3.6 0.9 1.0
O2B B:GDP202 3.6 1.0 1.0
PB B:GDP202 3.7 0.9 1.0
C B:SER20 3.7 0.9 1.0
NE2 A:GLN293 4.0 0.9 1.0
OE1 A:GLN293 4.0 0.9 1.0
CA B:GLY21 4.2 0.7 1.0
CD A:GLN293 4.4 0.9 1.0
OG B:SER20 4.4 0.4 1.0
NE A:ARG208 4.4 0.2 1.0
O3A B:GDP202 4.5 0.8 1.0
O2A B:GDP202 4.6 0.1 1.0
O B:SER20 4.7 0.9 1.0
O B:HOH301 4.8 88.5 1.0
N B:GLY69 4.8 0.4 1.0
CB B:SER42 4.8 0.2 1.0
OD1 A:ASP205 4.9 0.0 1.0
O3B B:GDP202 4.9 0.4 1.0
N B:SER20 5.0 0.9 1.0

Fluorine binding site 4 out of 6 in 4fme

Go back to Fluorine Binding Sites List in 4fme
Fluorine binding site 4 out of 6 in the Espg-RAB1-ARF6 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Espg-RAB1-ARF6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F201

b:0.1
occ:1.00
 F1 E:AF3201 0.0 0.1 1.0
AL E:AF3201 1.7 1.0 1.0
O2B E:GDP202 2.5 0.9 1.0
O D:HOH401 2.6 0.4 1.0
O1B E:GDP202 2.6 1.0 1.0
PB E:GDP202 2.9 1.0 1.0
F3 E:AF3201 2.9 0.7 1.0
F2 E:AF3201 3.0 0.9 1.0
O3B E:GDP202 3.3 0.3 1.0
NZ E:LYS24 3.3 0.8 1.0
MG E:MG203 3.4 91.4 1.0
CE E:LYS24 3.6 0.8 1.0
N E:GLY69 3.7 0.1 1.0
O E:THR67 3.8 0.3 1.0
CA E:ALA68 3.9 0.1 1.0
C E:ALA68 4.0 0.1 1.0
CA E:SER20 4.1 0.6 1.0
CB E:SER20 4.4 0.6 1.0
O3A E:GDP202 4.5 0.2 1.0
N E:GLY21 4.5 0.8 1.0
CA E:GLY69 4.5 0.1 1.0
O E:HOH301 4.5 87.0 1.0
C E:THR67 4.6 0.3 1.0
N E:ALA68 4.7 0.1 1.0
CB E:LYS24 4.8 0.8 1.0
CD E:LYS24 4.8 0.8 1.0
O E:ALA68 4.8 0.1 1.0
O E:ASP19 4.9 0.8 1.0
C E:SER20 4.9 0.6 1.0
CG E:LYS24 5.0 0.8 1.0
NH2 D:ARG208 5.0 0.7 1.0
CB E:ALA68 5.0 1.0 1.0

Fluorine binding site 5 out of 6 in 4fme

Go back to Fluorine Binding Sites List in 4fme
Fluorine binding site 5 out of 6 in the Espg-RAB1-ARF6 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Espg-RAB1-ARF6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F201

b:0.9
occ:1.00
 F2 E:AF3201 0.0 0.9 1.0
AL E:AF3201 1.7 1.0 1.0
O D:HOH401 2.6 0.4 1.0
O1B E:GDP202 2.6 1.0 1.0
O E:HOH301 2.7 87.0 1.0
N E:THR43 2.8 0.4 1.0
MG E:MG203 2.8 91.4 1.0
F3 E:AF3201 3.0 0.7 1.0
F1 E:AF3201 3.0 0.1 1.0
NH2 D:ARG208 3.2 0.7 1.0
CB E:THR43 3.2 0.9 1.0
CA E:THR43 3.5 0.4 1.0
O E:THR43 3.6 0.4 1.0
OG1 E:THR43 3.7 0.9 1.0
C E:SER42 3.8 0.3 1.0
PB E:GDP202 3.9 1.0 1.0
CA E:SER42 4.0 0.3 1.0
C E:THR43 4.0 0.4 1.0
CB E:SER42 4.2 0.7 1.0
O3B E:GDP202 4.3 0.3 1.0
OE1 D:GLN293 4.4 0.5 1.0
CZ D:ARG208 4.4 0.7 1.0
O2A E:GDP202 4.5 0.5 1.0
CG2 E:THR43 4.5 0.9 1.0
O2B E:GDP202 4.6 0.9 1.0
CA E:ALA68 4.8 0.1 1.0
NH1 D:ARG208 4.8 0.7 1.0
O E:SER42 4.9 0.3 1.0
OG E:SER25 5.0 0.1 1.0

Fluorine binding site 6 out of 6 in 4fme

Go back to Fluorine Binding Sites List in 4fme
Fluorine binding site 6 out of 6 in the Espg-RAB1-ARF6 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Espg-RAB1-ARF6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F201

b:0.7
occ:1.00
 F3 E:AF3201 0.0 0.7 1.0
AL E:AF3201 1.7 1.0 1.0
O D:HOH401 2.6 0.4 1.0
O1B E:GDP202 2.6 1.0 1.0
NH2 D:ARG208 2.8 0.7 1.0
NH1 D:ARG208 2.9 0.7 1.0
F1 E:AF3201 2.9 0.1 1.0
F2 E:AF3201 3.0 0.9 1.0
CZ D:ARG208 3.2 0.7 1.0
CB E:SER20 3.3 0.6 1.0
N E:GLY21 3.3 0.8 1.0
CA E:SER20 3.6 0.6 1.0
O2B E:GDP202 3.6 0.9 1.0
PB E:GDP202 3.7 1.0 1.0
C E:SER20 3.7 0.6 1.0
NE2 D:GLN293 4.0 0.5 1.0
OE1 D:GLN293 4.1 0.5 1.0
CA E:GLY21 4.2 0.8 1.0
OG E:SER20 4.4 0.6 1.0
CD D:GLN293 4.4 0.5 1.0
O3A E:GDP202 4.5 0.2 1.0
NE D:ARG208 4.5 0.7 1.0
O2A E:GDP202 4.6 0.5 1.0
O E:SER20 4.7 0.6 1.0
N E:GLY69 4.8 0.1 1.0
O E:HOH301 4.8 87.0 1.0
CB E:SER42 4.8 0.7 1.0
OD1 D:ASP205 4.9 0.7 1.0
O3B E:GDP202 4.9 0.3 1.0
N E:SER20 5.0 0.6 1.0

Reference:

N.Dong, Y.Zhu, Q.Lu, L.Hu, Y.Zheng, F.Shao. Structurally Distinct Bacterial Tbc-Like Gaps Link Arf Gtpase to RAB1 Inactivation to Counteract Host Defenses. Cell(Cambridge,Mass.) V. 150 1029 2012.
ISSN: ISSN 0092-8674
PubMed: 22939626
DOI: 10.1016/J.CELL.2012.06.050
Page generated: Thu Aug 1 01:37:41 2024

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