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Fluorine in PDB 4fmd: Espg-RAB1 Complex Structure at 3.05 A

Protein crystallography data

The structure of Espg-RAB1 Complex Structure at 3.05 A, PDB code: 4fmd 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 / 3.05
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 106.568, 153.221, 230.805, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 26.6

Other elements in 4fmd:

The structure of Espg-RAB1 Complex Structure at 3.05 A 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 Structure at 3.05 A (pdb code 4fmd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Espg-RAB1 Complex Structure at 3.05 A, PDB code: 4fmd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 4fmd

Go back to Fluorine Binding Sites List in 4fmd
Fluorine binding site 1 out of 9 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:48.9
occ:1.00
 F1 B:AF3201 0.0 48.9 1.0
AL B:AF3201 1.7 49.6 1.0
NZ B:LYS24 2.5 65.2 1.0
O A:HOH401 2.5 49.5 1.0
O2B B:GDP202 2.7 66.0 1.0
F3 B:AF3201 2.9 49.2 1.0
N B:GLY69 3.0 60.6 1.0
F2 B:AF3201 3.0 50.4 1.0
CE B:LYS24 3.4 64.0 1.0
CA B:SER20 3.4 66.4 1.0
O1B B:GDP202 3.5 57.6 1.0
PB B:GDP202 3.6 61.5 1.0
CA B:GLY69 3.7 60.1 1.0
CB B:SER20 3.8 67.5 1.0
O B:HOH301 3.8 41.1 1.0
CA B:ALA68 3.8 61.2 1.0
C B:ALA68 3.8 61.2 1.0
O B:THR67 3.9 61.1 1.0
MG B:MG203 4.1 53.1 1.0
N B:GLY21 4.1 66.4 1.0
O B:ASP19 4.2 65.2 1.0
O3B B:GDP202 4.2 61.2 1.0
N B:SER20 4.2 66.8 1.0
C B:SER20 4.3 67.0 1.0
C B:ASP19 4.5 65.9 1.0
O B:GLY18 4.6 64.6 1.0
C B:GLY69 4.7 61.2 1.0
C B:THR67 4.7 61.2 1.0
CB B:ALA68 4.7 62.5 1.0
N B:GLN70 4.7 61.7 1.0
N B:ALA68 4.8 61.2 1.0
CD B:LYS24 4.8 63.7 1.0
OE1 A:GLN293 4.9 55.1 1.0
OG B:SER20 4.9 68.6 1.0
O3A B:GDP202 5.0 62.9 1.0
O B:ALA68 5.0 62.1 1.0

Fluorine binding site 2 out of 9 in 4fmd

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Fluorine binding site 2 out of 9 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:50.4
occ:1.00
 F2 B:AF3201 0.0 50.4 1.0
AL B:AF3201 1.7 49.6 1.0
MG B:MG203 2.0 53.1 1.0
O A:HOH401 2.5 49.5 1.0
O2B B:GDP202 2.6 66.0 1.0
O3B B:GDP202 2.9 61.2 1.0
O B:HOH302 2.9 81.7 1.0
F3 B:AF3201 3.0 49.2 1.0
F1 B:AF3201 3.0 48.9 1.0
CB B:THR43 3.0 68.7 1.0
N B:THR43 3.2 72.2 1.0
O B:HOH301 3.2 41.1 1.0
PB B:GDP202 3.3 61.5 1.0
OG1 B:THR43 3.3 68.0 1.0
CA B:THR43 3.6 70.4 1.0
NH2 A:ARG208 3.7 70.6 1.0
OG B:SER25 4.1 64.2 1.0
CG2 B:THR43 4.2 68.3 1.0
O B:THR43 4.2 70.2 1.0
O1B B:GDP202 4.2 57.6 1.0
C B:SER42 4.3 75.1 1.0
C B:THR43 4.4 70.5 1.0
O1A B:GDP202 4.5 61.7 1.0
CA B:SER42 4.5 77.1 1.0
CZ A:ARG208 4.5 70.5 1.0
CB B:SER42 4.5 77.5 1.0
O3A B:GDP202 4.5 62.9 1.0
O B:THR67 4.8 61.1 1.0
NH1 A:ARG208 4.8 71.2 1.0
CA B:ALA68 4.8 61.2 1.0
NZ B:LYS24 4.9 65.2 1.0

Fluorine binding site 3 out of 9 in 4fmd

Go back to Fluorine Binding Sites List in 4fmd
Fluorine binding site 3 out of 9 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:49.2
occ:1.00
 F3 B:AF3201 0.0 49.2 1.0
AL B:AF3201 1.7 49.6 1.0
O A:HOH401 2.6 49.5 1.0
O2B B:GDP202 2.7 66.0 1.0
NH1 A:ARG208 2.7 71.2 1.0
F1 B:AF3201 2.9 48.9 1.0
F2 B:AF3201 3.0 50.4 1.0
NH2 A:ARG208 3.0 70.6 1.0
NE2 A:GLN293 3.1 56.9 1.0
CB B:SER20 3.2 67.5 1.0
CZ A:ARG208 3.3 70.5 1.0
OG B:SER20 3.5 68.6 1.0
CA B:SER20 3.7 66.4 1.0
N B:GLY21 3.8 66.4 1.0
OE1 A:GLN293 3.9 55.1 1.0
CD A:GLN293 4.0 55.8 1.0
C B:SER20 4.1 67.0 1.0
PB B:GDP202 4.2 61.5 1.0
OD1 A:ASP205 4.4 67.8 1.0
CB B:SER42 4.5 77.5 1.0
NE A:ARG208 4.6 70.0 1.0
CA B:GLY21 4.7 67.0 1.0
OG B:SER42 4.8 79.6 1.0
MG B:MG203 4.8 53.1 1.0
O3B B:GDP202 4.8 61.2 1.0
N B:THR43 4.9 72.2 1.0
N B:GLY69 4.9 60.6 1.0
O3A B:GDP202 5.0 62.9 1.0

Fluorine binding site 4 out of 9 in 4fmd

Go back to Fluorine Binding Sites List in 4fmd
Fluorine binding site 4 out of 9 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F201

b:51.0
occ:1.00
 F1 D:AF3201 0.0 51.0 1.0
AL D:AF3201 1.7 51.7 1.0
O C:HOH501 2.6 51.2 1.0
O3B D:GDP202 2.7 82.6 1.0
F2 D:AF3201 2.9 51.2 1.0
F3 D:AF3201 3.0 50.8 1.0
NZ D:LYS24 3.0 80.0 1.0
N D:GLY69 3.0 70.2 1.0
O2B D:GDP202 3.1 79.3 1.0
PB D:GDP202 3.3 80.7 1.0
CA D:SER20 3.4 80.8 1.0
O D:THR67 3.5 71.6 1.0
MG D:MG203 3.6 69.4 1.0
CA D:GLY69 3.7 70.7 1.0
O D:ASP19 3.7 80.8 1.0
CB D:SER20 3.8 80.0 1.0
CE D:LYS24 3.8 79.1 1.0
O D:HOH301 3.8 75.7 1.0
C D:ALA68 3.9 69.2 1.0
N D:GLY21 3.9 83.7 1.0
O1B D:GDP202 3.9 78.8 1.0
CA D:ALA68 3.9 69.3 1.0
C D:SER20 4.2 83.2 1.0
N D:SER20 4.2 81.2 1.0
C D:ASP19 4.3 81.3 1.0
C D:THR67 4.5 70.4 1.0
N D:ALA68 4.7 69.3 1.0
O3A D:GDP202 4.8 84.3 1.0
C D:GLY69 4.9 70.6 1.0
N D:GLN70 4.9 70.0 1.0
OE1 C:GLN293 5.0 69.7 1.0

Fluorine binding site 5 out of 9 in 4fmd

Go back to Fluorine Binding Sites List in 4fmd
Fluorine binding site 5 out of 9 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F201

b:51.2
occ:1.00
 F2 D:AF3201 0.0 51.2 1.0
AL D:AF3201 1.7 51.7 1.0
MG D:MG203 2.0 69.4 1.0
O C:HOH501 2.4 51.2 1.0
O3B D:GDP202 2.7 82.6 1.0
O D:HOH302 2.7 76.2 1.0
F1 D:AF3201 2.9 51.0 1.0
N D:THR43 3.0 83.5 1.0
F3 D:AF3201 3.0 50.8 1.0
CB D:THR43 3.1 80.2 1.0
O1B D:GDP202 3.2 78.8 1.0
O D:HOH301 3.2 75.7 1.0
PB D:GDP202 3.5 80.7 1.0
CA D:THR43 3.5 80.9 1.0
OG1 D:THR43 3.5 81.7 1.0
NH2 C:ARG208 3.7 88.6 1.0
O D:THR43 3.8 78.3 1.0
C D:SER42 4.1 85.9 1.0
C D:THR43 4.2 78.7 1.0
OG D:SER25 4.2 79.5 1.0
CG2 D:THR43 4.3 79.3 1.0
CA D:SER42 4.4 88.7 1.0
O2B D:GDP202 4.4 79.3 1.0
O2A D:GDP202 4.4 83.6 1.0
CA D:ALA68 4.6 69.3 1.0
O D:THR67 4.6 71.6 1.0
CB D:SER42 4.7 88.2 1.0
CZ C:ARG208 4.7 88.4 1.0
O3A D:GDP202 4.8 84.3 1.0
OE1 C:GLN293 4.9 69.7 1.0
NH1 C:ARG208 5.0 87.5 1.0

Fluorine binding site 6 out of 9 in 4fmd

Go back to Fluorine Binding Sites List in 4fmd
Fluorine binding site 6 out of 9 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F201

b:50.8
occ:1.00
 F3 D:AF3201 0.0 50.8 1.0
AL D:AF3201 1.7 51.7 1.0
O C:HOH501 2.3 51.2 1.0
O3B D:GDP202 2.6 82.6 1.0
NH1 C:ARG208 2.9 87.5 1.0
F1 D:AF3201 3.0 51.0 1.0
F2 D:AF3201 3.0 51.2 1.0
NH2 C:ARG208 3.1 88.6 1.0
CB D:SER20 3.2 80.0 1.0
NE2 C:GLN293 3.2 72.3 1.0
CZ C:ARG208 3.4 88.4 1.0
N D:GLY21 3.5 83.7 1.0
CA D:SER20 3.6 80.8 1.0
OG D:SER20 3.9 82.1 1.0
C D:SER20 3.9 83.2 1.0
OE1 C:GLN293 4.1 69.7 1.0
CD C:GLN293 4.1 70.3 1.0
PB D:GDP202 4.1 80.7 1.0
OD1 C:ASP205 4.3 84.5 1.0
CA D:GLY21 4.4 86.4 1.0
CB D:SER42 4.5 88.2 1.0
MG D:MG203 4.6 69.4 1.0
NE C:ARG208 4.8 89.2 1.0
O2B D:GDP202 4.8 79.3 1.0
O D:HOH302 4.9 76.2 1.0
N D:GLY69 4.9 70.2 1.0
O1B D:GDP202 4.9 78.8 1.0
N D:THR43 4.9 83.5 1.0
O3A D:GDP202 5.0 84.3 1.0

Fluorine binding site 7 out of 9 in 4fmd

Go back to Fluorine Binding Sites List in 4fmd
Fluorine binding site 7 out of 9 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:62.4
occ:1.00
 F1 F:AF3201 0.0 62.4 1.0
AL F:AF3201 1.7 62.5 1.0
O1B F:GDP202 2.6 0.3 1.0
O E:HOH501 2.7 62.4 1.0
NZ F:LYS24 2.8 0.4 1.0
F3 F:AF3201 3.0 62.4 1.0
O2B F:GDP202 3.0 0.3 1.0
F2 F:AF3201 3.0 62.5 1.0
N F:GLY69 3.2 0.2 1.0
PB F:GDP202 3.2 0.0 1.0
CA F:SER20 3.3 0.9 1.0
O F:ASP19 3.5 0.6 1.0
CA F:GLY69 3.6 0.7 1.0
N F:GLY21 3.6 0.5 1.0
CE F:LYS24 3.7 0.8 1.0
O F:HOH301 3.8 92.6 1.0
O3B F:GDP202 3.8 0.4 1.0
CB F:SER20 4.0 0.9 1.0
O F:THR67 4.0 1.0 1.0
C F:SER20 4.0 0.7 1.0
N F:SER20 4.1 0.2 1.0
C F:ASP19 4.2 0.4 1.0
C F:ALA68 4.2 0.3 1.0
MG F:MG203 4.3 91.3 1.0
CA F:ALA68 4.4 0.7 1.0
O3A F:GDP202 4.7 0.9 1.0
C F:GLY69 4.8 1.0 1.0
CA F:GLY21 4.9 0.6 1.0
NH2 E:ARG208 4.9 0.8 1.0
O F:GLY18 5.0 0.5 1.0

Fluorine binding site 8 out of 9 in 4fmd

Go back to Fluorine Binding Sites List in 4fmd
Fluorine binding site 8 out of 9 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:62.5
occ:1.00
 F2 F:AF3201 0.0 62.5 1.0
AL F:AF3201 1.7 62.5 1.0
MG F:MG203 2.2 91.3 1.0
O E:HOH501 2.6 62.4 1.0
O1B F:GDP202 2.7 0.3 1.0
O3B F:GDP202 2.9 0.4 1.0
F3 F:AF3201 3.0 62.4 1.0
F1 F:AF3201 3.0 62.4 1.0
OG1 F:THR43 3.0 0.8 1.0
N F:THR43 3.1 0.8 1.0
CB F:THR43 3.2 0.9 1.0
PB F:GDP202 3.3 0.0 1.0
O F:HOH301 3.5 92.6 1.0
NH2 E:ARG208 3.7 0.8 1.0
CA F:THR43 3.7 0.2 1.0
O2A F:GDP202 3.8 0.4 1.0
OG F:SER25 4.1 0.7 1.0
C F:SER42 4.2 0.4 1.0
O2B F:GDP202 4.2 0.3 1.0
O F:THR43 4.3 0.4 1.0
CA F:SER42 4.4 0.2 1.0
CZ E:ARG208 4.5 0.8 1.0
C F:THR43 4.5 0.4 1.0
CG2 F:THR43 4.6 0.4 1.0
O3A F:GDP202 4.6 0.9 1.0
CB F:SER42 4.6 0.3 1.0
NH1 E:ARG208 4.8 0.5 1.0
O F:THR67 4.8 1.0 1.0
PA F:GDP202 4.9 0.7 1.0

Fluorine binding site 9 out of 9 in 4fmd

Go back to Fluorine Binding Sites List in 4fmd
Fluorine binding site 9 out of 9 in the Espg-RAB1 Complex Structure at 3.05 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Espg-RAB1 Complex Structure at 3.05 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:62.4
occ:1.00
 F3 F:AF3201 0.0 62.4 1.0
AL F:AF3201 1.7 62.5 1.0
O E:HOH501 2.1 62.4 1.0
O1B F:GDP202 2.6 0.3 1.0
NH2 E:ARG208 2.7 0.8 1.0
NH1 E:ARG208 2.8 0.5 1.0
F1 F:AF3201 3.0 62.4 1.0
F2 F:AF3201 3.0 62.5 1.0
N F:GLY21 3.1 0.5 1.0
CZ E:ARG208 3.1 0.8 1.0
CB F:SER20 3.4 0.9 1.0
CA F:SER20 3.5 0.9 1.0
NE2 E:GLN293 3.6 89.3 1.0
C F:SER20 3.6 0.7 1.0
CA F:GLY21 3.9 0.6 1.0
PB F:GDP202 4.1 0.0 1.0
OE1 E:GLN293 4.3 89.5 1.0
CD E:GLN293 4.4 88.1 1.0
OG F:SER20 4.4 0.6 1.0
NE E:ARG208 4.4 0.8 1.0
OD1 E:ASP205 4.6 98.3 1.0
O F:SER20 4.7 0.9 1.0
O2A F:GDP202 4.7 0.4 1.0
CB F:SER42 4.7 0.3 1.0
O2B F:GDP202 4.8 0.3 1.0
O3B F:GDP202 4.8 0.4 1.0
N F:SER20 4.9 0.2 1.0
N F:GLY69 5.0 0.2 1.0
OG F:SER42 5.0 0.7 1.0
MG F:MG203 5.0 91.3 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: Thu Aug 1 01:37:35 2024

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