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:
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
Go back to
Fluorine Binding Sites List in 4fmc
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: Thu Aug 1 01:37:31 2024
|