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Fluorine in PDB 4fmc: Espg-RAB1 Complex

Protein crystallography data

The structure of Espg-RAB1 Complex, PDB code: 4fmc 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 / 2.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 107.566, 152.707, 226.706, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 27.7

Other elements in 4fmc:

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

Magnesium (Mg) 3 atoms
Aluminium (Al) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Espg-RAB1 Complex (pdb code 4fmc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Espg-RAB1 Complex, PDB code: 4fmc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4fmc

Go back to Fluorine Binding Sites List in 4fmc
Fluorine binding site 1 out of 8 in the Espg-RAB1 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:36.9
occ:1.00
F1 B:AF3201 0.0 36.9 1.0
AL B:AF3201 1.7 39.1 1.0
NZ B:LYS24 2.6 44.2 1.0
O1B B:GDP202 2.6 49.8 1.0
O A:HOH501 2.6 36.9 1.0
F3 B:AF3201 2.9 38.1 1.0
F2 B:AF3201 3.0 38.5 1.0
N B:GLY69 3.0 51.1 1.0
O B:HOH301 3.3 71.2 1.0
CA B:SER20 3.3 55.4 1.0
CE B:LYS24 3.5 45.0 1.0
PB B:GDP202 3.5 48.6 1.0
O2B B:GDP202 3.6 46.5 1.0
CA B:ALA68 3.7 52.0 1.0
C B:ALA68 3.8 51.7 1.0
O B:THR67 3.8 52.1 1.0
CA B:GLY69 3.9 50.5 1.0
CB B:SER20 3.9 56.5 1.0
N B:SER20 4.0 55.8 1.0
O B:ASP19 4.0 54.8 1.0
O3B B:GDP202 4.1 46.7 1.0
N B:GLY21 4.3 54.5 1.0
MG B:MG203 4.3 52.6 1.0
C B:SER20 4.3 55.3 1.0
C B:ASP19 4.3 55.1 1.0
OG B:SER20 4.5 58.3 1.0
O B:GLY18 4.6 53.7 1.0
CB B:ALA68 4.7 53.1 1.0
C B:THR67 4.7 52.2 1.0
N B:ALA68 4.7 52.6 1.0
C B:GLY69 4.7 51.9 1.0
OE1 A:GLN293 4.8 53.3 1.0
N B:GLN70 4.9 52.2 1.0
CD B:LYS24 4.9 45.2 1.0
O B:ALA68 5.0 52.9 1.0
O3A B:GDP202 5.0 47.9 1.0

Fluorine binding site 2 out of 8 in 4fmc

Go back to Fluorine Binding Sites List in 4fmc
Fluorine binding site 2 out of 8 in the Espg-RAB1 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:38.5
occ:1.00
F2 B:AF3201 0.0 38.5 1.0
AL B:AF3201 1.7 39.1 1.0
MG B:MG203 2.3 52.6 1.0
O B:HOH302 2.5 44.9 1.0
O3B B:GDP202 2.6 46.7 1.0
O A:HOH501 2.6 36.9 1.0
O1B B:GDP202 2.7 49.8 1.0
O B:HOH301 2.8 71.2 1.0
F1 B:AF3201 3.0 36.9 1.0
F3 B:AF3201 3.1 38.1 1.0
OG1 B:THR43 3.1 54.0 1.0
PB B:GDP202 3.1 48.6 1.0
CB B:THR43 3.2 55.1 1.0
N B:THR43 3.3 58.4 1.0
NH2 A:ARG208 3.8 62.8 1.0
CA B:THR43 3.8 56.6 1.0
OG B:SER25 3.8 48.2 1.0
O1A B:GDP202 4.2 48.7 1.0
O2B B:GDP202 4.2 46.5 1.0
O B:THR43 4.3 56.3 1.0
C B:SER42 4.4 61.3 1.0
O3A B:GDP202 4.4 47.9 1.0
CG2 B:THR43 4.5 54.8 1.0
C B:THR43 4.5 56.3 1.0
CA B:SER42 4.6 63.2 1.0
O B:THR67 4.6 52.1 1.0
CZ A:ARG208 4.7 63.7 1.0
CB B:SER42 4.7 63.3 1.0
NZ B:LYS24 4.7 44.2 1.0
PA B:GDP202 4.8 49.2 1.0
CA B:ALA68 4.8 52.0 1.0

Fluorine binding site 3 out of 8 in 4fmc

Go back to Fluorine Binding Sites List in 4fmc
Fluorine binding site 3 out of 8 in the Espg-RAB1 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:38.1
occ:1.00
F3 B:AF3201 0.0 38.1 1.0
AL B:AF3201 1.7 39.1 1.0
O A:HOH501 2.5 36.9 1.0
O1B B:GDP202 2.7 49.8 1.0
F1 B:AF3201 2.9 36.9 1.0
OG B:SER20 3.0 58.3 1.0
F2 B:AF3201 3.1 38.5 1.0
NH1 A:ARG208 3.1 63.0 1.0
NH2 A:ARG208 3.2 62.8 1.0
NE2 A:GLN293 3.2 54.9 1.0
CB B:SER20 3.4 56.5 1.0
CZ A:ARG208 3.5 63.7 1.0
CA B:SER20 3.6 55.4 1.0
N B:GLY21 3.8 54.5 1.0
OE1 A:GLN293 3.9 53.3 1.0
CD A:GLN293 3.9 53.4 1.0
PB B:GDP202 4.1 48.6 1.0
C B:SER20 4.1 55.3 1.0
CB B:SER42 4.4 63.3 1.0
OD1 A:ASP205 4.5 59.5 1.0
O3B B:GDP202 4.7 46.7 1.0
OG B:SER42 4.8 65.6 1.0
NE A:ARG208 4.8 64.6 1.0
CA B:GLY21 4.8 55.4 1.0
N B:THR43 4.9 58.4 1.0
N B:SER20 4.9 55.8 1.0
O B:HOH302 5.0 44.9 1.0
N B:GLY69 5.0 51.1 1.0
O3A B:GDP202 5.0 47.9 1.0

Fluorine binding site 4 out of 8 in 4fmc

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Fluorine binding site 4 out of 8 in the Espg-RAB1 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F201

b:37.0
occ:1.00
F1 D:AF3201 0.0 37.0 1.0
AL D:AF3201 1.7 38.9 1.0
O C:HOH401 2.6 68.7 1.0
NZ D:LYS24 2.6 64.2 1.0
O3B D:GDP202 2.7 73.3 1.0
F2 D:AF3201 2.9 38.3 1.0
F3 D:AF3201 2.9 38.2 1.0
N D:GLY69 3.1 63.3 1.0
O2B D:GDP202 3.4 70.0 1.0
CA D:SER20 3.4 74.8 1.0
PB D:GDP202 3.5 72.3 1.0
MG D:MG203 3.6 78.1 1.0
O D:THR67 3.6 67.1 1.0
CE D:LYS24 3.7 65.1 1.0
CA D:GLY69 3.8 63.4 1.0
CB D:SER20 3.8 74.3 1.0
O1B D:GDP202 3.9 70.1 1.0
C D:ALA68 4.0 62.5 1.0
CA D:ALA68 4.0 63.4 1.0
N D:GLY21 4.1 78.1 1.0
OG D:SER20 4.1 76.8 1.0
C D:SER20 4.3 77.5 1.0
N D:SER20 4.3 74.6 1.0
O D:ASP19 4.5 76.4 1.0
C D:THR67 4.6 65.5 1.0
C D:GLY69 4.7 63.5 1.0
OE1 C:GLN293 4.7 65.3 1.0
C D:ASP19 4.7 75.4 1.0
NH2 C:ARG208 4.8 87.8 1.0
N D:ALA68 4.8 63.9 1.0
O D:GLY18 4.8 71.9 1.0
N D:GLN70 4.9 63.3 1.0
OG1 D:THR43 4.9 73.6 1.0
O3A D:GDP202 5.0 77.7 1.0

Fluorine binding site 5 out of 8 in 4fmc

Go back to Fluorine Binding Sites List in 4fmc
Fluorine binding site 5 out of 8 in the Espg-RAB1 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F201

b:38.3
occ:1.00
F2 D:AF3201 0.0 38.3 1.0
AL D:AF3201 1.7 38.9 1.0
MG D:MG203 2.1 78.1 1.0
O1B D:GDP202 2.5 70.1 1.0
OG1 D:THR43 2.6 73.6 1.0
O3B D:GDP202 2.6 73.3 1.0
O C:HOH401 2.6 68.7 1.0
O D:HOH301 2.8 58.2 1.0
F1 D:AF3201 2.9 37.0 1.0
PB D:GDP202 3.0 72.3 1.0
F3 D:AF3201 3.0 38.2 1.0
CB D:THR43 3.1 73.2 1.0
N D:THR43 3.2 77.8 1.0
NH2 C:ARG208 3.2 87.8 1.0
O2A D:GDP202 3.7 79.1 1.0
CA D:THR43 3.7 74.2 1.0
OG D:SER25 3.7 73.4 1.0
O2B D:GDP202 4.1 70.0 1.0
C D:SER42 4.3 81.2 1.0
O3A D:GDP202 4.4 77.7 1.0
CG2 D:THR43 4.5 72.3 1.0
O D:THR43 4.5 70.1 1.0
CZ C:ARG208 4.5 88.5 1.0
CA D:SER42 4.5 84.7 1.0
C D:THR43 4.6 71.5 1.0
O D:THR67 4.6 67.1 1.0
PA D:GDP202 4.6 81.3 1.0
NZ D:LYS24 4.7 64.2 1.0
CB D:SER25 4.9 77.1 1.0
CB D:SER42 5.0 83.9 1.0

Fluorine binding site 6 out of 8 in 4fmc

Go back to Fluorine Binding Sites List in 4fmc
Fluorine binding site 6 out of 8 in the Espg-RAB1 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F201

b:38.2
occ:1.00
F3 D:AF3201 0.0 38.2 1.0
AL D:AF3201 1.7 38.9 1.0
OG D:SER20 2.6 76.8 1.0
NH2 C:ARG208 2.6 87.8 1.0
O C:HOH401 2.6 68.7 1.0
O3B D:GDP202 2.7 73.3 1.0
F1 D:AF3201 2.9 37.0 1.0
F2 D:AF3201 3.0 38.3 1.0
NE2 C:GLN293 3.3 69.8 1.0
CB D:SER20 3.4 74.3 1.0
CZ C:ARG208 3.5 88.5 1.0
NH1 C:ARG208 3.5 87.5 1.0
N D:GLY21 3.8 78.1 1.0
CA D:SER20 3.8 74.8 1.0
OE1 C:GLN293 4.0 65.3 1.0
CD C:GLN293 4.0 66.6 1.0
C D:SER20 4.1 77.5 1.0
PB D:GDP202 4.1 72.3 1.0
CB D:SER42 4.5 83.9 1.0
CA D:GLY21 4.6 81.6 1.0
OD1 C:ASP205 4.7 79.5 1.0
NE C:ARG208 4.7 90.9 1.0
O1B D:GDP202 4.7 70.1 1.0
N D:THR43 4.7 77.8 1.0
O2A D:GDP202 4.9 79.1 1.0
O2B D:GDP202 4.9 70.0 1.0
MG D:MG203 5.0 78.1 1.0
N D:GLY69 5.0 63.3 1.0

Fluorine binding site 7 out of 8 in 4fmc

Go back to Fluorine Binding Sites List in 4fmc
Fluorine binding site 7 out of 8 in the Espg-RAB1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Espg-RAB1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:34.6
occ:1.00
F2 F:AF3201 0.0 34.6 1.0
AL F:AF3201 1.7 34.5 1.0
O2B F:GDP202 2.6 0.9 1.0
OG1 F:THR43 2.7 0.7 1.0
MG F:MG203 2.8 0.8 1.0
CB F:THR43 2.8 0.2 1.0
F3 F:AF3201 3.0 34.4 1.0
N F:THR43 3.2 0.8 1.0
O3B F:GDP202 3.5 0.0 1.0
CA F:THR43 3.5 0.9 1.0
PB F:GDP202 3.5 0.2 1.0
O F:THR43 3.8 0.3 1.0
NH2 E:ARG208 3.9 0.2 1.0
O F:THR67 4.1 0.1 1.0
O1B F:GDP202 4.1 0.6 1.0
CG2 F:THR43 4.2 0.3 1.0
C F:THR43 4.2 0.5 1.0
C F:SER42 4.4 1.0 1.0
NZ F:LYS24 4.4 0.7 1.0
CA F:ALA68 4.4 0.2 1.0
OG F:SER25 4.7 0.0 1.0
CA F:SER42 4.7 0.5 1.0
N F:GLY21 4.8 0.4 1.0
C F:THR67 4.9 0.0 1.0
CB F:SER42 5.0 0.6 1.0
N F:ALA68 5.0 0.8 1.0

Fluorine binding site 8 out of 8 in 4fmc

Go back to Fluorine Binding Sites List in 4fmc
Fluorine binding site 8 out of 8 in the Espg-RAB1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Espg-RAB1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:34.4
occ:1.00
F3 F:AF3201 0.0 34.4 1.0
AL F:AF3201 1.7 34.5 1.0
NH2 E:ARG208 2.6 0.2 1.0
N F:GLY21 2.7 0.4 1.0
O2B F:GDP202 2.7 0.9 1.0
OG F:SER20 2.9 0.8 1.0
F2 F:AF3201 3.0 34.6 1.0
CA F:SER20 3.3 0.8 1.0
C F:SER20 3.4 0.1 1.0
CA F:GLY21 3.5 0.7 1.0
NE2 E:GLN293 3.6 0.9 1.0
CB F:SER20 3.6 0.0 1.0
CZ E:ARG208 3.8 0.6 1.0
PB F:GDP202 4.0 0.2 1.0
O1B F:GDP202 4.1 0.6 1.0
NH1 E:ARG208 4.3 0.1 1.0
CD E:GLN293 4.4 0.5 1.0
OE1 E:GLN293 4.4 0.1 1.0
O F:SER20 4.5 0.3 1.0
N F:SER20 4.7 0.8 1.0
N F:GLY69 4.7 0.1 1.0
O F:ASP19 4.7 0.7 1.0
CB F:SER42 4.8 0.6 1.0
NE E:ARG208 4.9 0.4 1.0
C F:GLY21 4.9 0.4 1.0
OG F:SER42 5.0 0.3 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: Sun Dec 13 12:02:39 2020

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