Fluorine in PDB 3ex7: The Crystal Structure of Ejc in Its Transition State
Protein crystallography data
The structure of The Crystal Structure of Ejc in Its Transition State, PDB code: 3ex7
was solved by
G.R.Andersen,
K.H.Nielsen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.06 /
2.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
182.040,
100.750,
145.880,
90.00,
112.08,
90.00
|
R / Rfree (%)
|
20.6 /
25.1
|
Other elements in 3ex7:
The structure of The Crystal Structure of Ejc in Its Transition State also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the The Crystal Structure of Ejc in Its Transition State
(pdb code 3ex7). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
The Crystal Structure of Ejc in Its Transition State, PDB code: 3ex7:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 3ex7
Go back to
Fluorine Binding Sites List in 3ex7
Fluorine binding site 1 out
of 6 in the The Crystal Structure of Ejc in Its Transition State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of The Crystal Structure of Ejc in Its Transition State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F415
b:60.1
occ:1.00
|
F1
|
C:AF3415
|
0.0
|
60.1
|
1.0
|
AL
|
C:AF3415
|
1.8
|
0.3
|
1.0
|
NH2
|
C:ARG367
|
2.6
|
25.4
|
1.0
|
NH1
|
C:ARG370
|
2.9
|
30.1
|
1.0
|
O
|
C:HOH461
|
3.0
|
25.5
|
1.0
|
F2
|
C:AF3415
|
3.1
|
37.4
|
1.0
|
F3
|
C:AF3415
|
3.1
|
42.1
|
1.0
|
O3B
|
C:ADP414
|
3.3
|
34.6
|
1.0
|
CB
|
C:SER84
|
3.3
|
33.1
|
1.0
|
NH1
|
C:ARG367
|
3.4
|
27.4
|
1.0
|
CZ
|
C:ARG367
|
3.4
|
27.0
|
1.0
|
N
|
C:GLY85
|
3.7
|
25.3
|
1.0
|
CA
|
C:SER84
|
3.7
|
25.5
|
1.0
|
CZ
|
C:ARG370
|
3.9
|
37.2
|
1.0
|
NH2
|
C:ARG370
|
4.1
|
35.3
|
1.0
|
C
|
C:SER84
|
4.2
|
38.1
|
1.0
|
O
|
C:GLY366
|
4.2
|
25.3
|
1.0
|
N
|
C:GLY340
|
4.3
|
30.6
|
1.0
|
OG
|
C:SER84
|
4.4
|
43.9
|
1.0
|
CA
|
C:GLY340
|
4.5
|
15.9
|
1.0
|
CA
|
C:GLY85
|
4.6
|
26.8
|
1.0
|
NE
|
C:ARG367
|
4.7
|
27.4
|
1.0
|
PB
|
C:ADP414
|
4.7
|
32.0
|
1.0
|
C
|
C:GLY366
|
4.7
|
31.6
|
1.0
|
ND1
|
C:HIS363
|
4.8
|
22.7
|
1.0
|
O
|
C:HOH417
|
4.9
|
27.0
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 3ex7
Go back to
Fluorine Binding Sites List in 3ex7
Fluorine binding site 2 out
of 6 in the The Crystal Structure of Ejc in Its Transition State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of The Crystal Structure of Ejc in Its Transition State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F415
b:37.4
occ:1.00
|
F2
|
C:AF3415
|
0.0
|
37.4
|
1.0
|
AL
|
C:AF3415
|
1.8
|
0.3
|
1.0
|
O
|
C:HOH569
|
2.6
|
27.9
|
1.0
|
O
|
C:HOH417
|
2.9
|
27.0
|
1.0
|
F1
|
C:AF3415
|
3.1
|
60.1
|
1.0
|
F3
|
C:AF3415
|
3.1
|
42.1
|
1.0
|
NZ
|
C:LYS88
|
3.1
|
20.7
|
1.0
|
CA
|
C:SER84
|
3.4
|
25.5
|
1.0
|
O3B
|
C:ADP414
|
3.5
|
34.6
|
1.0
|
CB
|
C:ALA219
|
3.5
|
24.0
|
1.0
|
O
|
C:HOH461
|
3.7
|
25.5
|
1.0
|
CB
|
C:SER84
|
3.9
|
33.1
|
1.0
|
O2B
|
C:ADP414
|
4.0
|
25.6
|
1.0
|
CE
|
C:LYS88
|
4.0
|
40.7
|
1.0
|
PB
|
C:ADP414
|
4.0
|
32.0
|
1.0
|
N
|
C:GLY85
|
4.1
|
25.3
|
1.0
|
N
|
C:ALA219
|
4.1
|
29.2
|
1.0
|
N
|
C:SER84
|
4.1
|
28.9
|
1.0
|
O
|
C:HOH571
|
4.3
|
33.4
|
1.0
|
O
|
C:GLN83
|
4.3
|
31.7
|
1.0
|
C
|
C:SER84
|
4.3
|
38.1
|
1.0
|
CA
|
C:ALA219
|
4.3
|
30.2
|
1.0
|
O1B
|
C:ADP414
|
4.4
|
28.5
|
1.0
|
O
|
C:SER82
|
4.4
|
21.5
|
1.0
|
C
|
C:GLN83
|
4.4
|
33.4
|
1.0
|
MG
|
C:MG416
|
4.7
|
32.7
|
1.0
|
CE1
|
C:HIS363
|
4.8
|
32.6
|
1.0
|
ND1
|
C:HIS363
|
4.8
|
22.7
|
1.0
|
OE1
|
C:GLU188
|
4.8
|
33.4
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 3ex7
Go back to
Fluorine Binding Sites List in 3ex7
Fluorine binding site 3 out
of 6 in the The Crystal Structure of Ejc in Its Transition State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of The Crystal Structure of Ejc in Its Transition State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F415
b:42.1
occ:1.00
|
F3
|
C:AF3415
|
0.0
|
42.1
|
1.0
|
AL
|
C:AF3415
|
1.8
|
0.3
|
1.0
|
MG
|
C:MG416
|
2.2
|
32.7
|
1.0
|
O3B
|
C:ADP414
|
2.7
|
34.6
|
1.0
|
O1B
|
C:ADP414
|
3.0
|
28.5
|
1.0
|
O
|
C:HOH572
|
3.1
|
22.9
|
1.0
|
O
|
C:HOH570
|
3.1
|
34.6
|
1.0
|
F1
|
C:AF3415
|
3.1
|
60.1
|
1.0
|
O
|
C:HOH571
|
3.1
|
33.4
|
1.0
|
F2
|
C:AF3415
|
3.1
|
37.4
|
1.0
|
O
|
C:HOH461
|
3.3
|
25.5
|
1.0
|
OE1
|
C:GLU188
|
3.3
|
33.4
|
1.0
|
PB
|
C:ADP414
|
3.4
|
32.0
|
1.0
|
CA
|
C:GLY340
|
3.4
|
15.9
|
1.0
|
N
|
C:GLY340
|
3.9
|
30.6
|
1.0
|
O
|
C:HOH417
|
3.9
|
27.0
|
1.0
|
NZ
|
C:LYS88
|
4.1
|
20.7
|
1.0
|
O
|
C:GLY340
|
4.2
|
29.2
|
1.0
|
C
|
C:GLY340
|
4.3
|
25.7
|
1.0
|
NH2
|
C:ARG370
|
4.3
|
35.3
|
1.0
|
OG1
|
C:THR89
|
4.4
|
31.2
|
1.0
|
O2B
|
C:ADP414
|
4.4
|
25.6
|
1.0
|
CD
|
C:GLU188
|
4.5
|
38.0
|
1.0
|
O
|
C:HOH569
|
4.6
|
27.9
|
1.0
|
O3A
|
C:ADP414
|
4.7
|
36.5
|
1.0
|
NH1
|
C:ARG370
|
4.8
|
30.1
|
1.0
|
O2A
|
C:ADP414
|
4.8
|
22.1
|
1.0
|
NH2
|
C:ARG367
|
4.9
|
25.4
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 3ex7
Go back to
Fluorine Binding Sites List in 3ex7
Fluorine binding site 4 out
of 6 in the The Crystal Structure of Ejc in Its Transition State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of The Crystal Structure of Ejc in Its Transition State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F415
b:52.0
occ:1.00
|
F1
|
H:AF3415
|
0.0
|
52.0
|
1.0
|
AL
|
H:AF3415
|
1.8
|
0.4
|
1.0
|
NH2
|
H:ARG367
|
2.9
|
63.7
|
1.0
|
NH1
|
H:ARG370
|
3.0
|
57.3
|
1.0
|
O3B
|
H:ADP414
|
3.0
|
52.4
|
1.0
|
O
|
H:HOH421
|
3.0
|
47.8
|
1.0
|
F3
|
H:AF3415
|
3.1
|
66.6
|
1.0
|
F2
|
H:AF3415
|
3.1
|
72.9
|
1.0
|
NH1
|
H:ARG367
|
3.3
|
66.4
|
1.0
|
CB
|
H:SER84
|
3.5
|
52.4
|
1.0
|
CZ
|
H:ARG367
|
3.5
|
66.2
|
1.0
|
N
|
H:GLY85
|
3.6
|
55.6
|
1.0
|
CZ
|
H:ARG370
|
3.8
|
65.5
|
1.0
|
CA
|
H:SER84
|
3.9
|
51.2
|
1.0
|
NH2
|
H:ARG370
|
3.9
|
51.3
|
1.0
|
O
|
H:GLY366
|
4.1
|
65.2
|
1.0
|
C
|
H:SER84
|
4.2
|
55.7
|
1.0
|
OG
|
H:SER84
|
4.2
|
58.5
|
1.0
|
N
|
H:GLY340
|
4.3
|
61.2
|
1.0
|
CA
|
H:GLY340
|
4.4
|
60.0
|
1.0
|
PB
|
H:ADP414
|
4.4
|
49.0
|
1.0
|
CA
|
H:GLY85
|
4.5
|
46.5
|
1.0
|
O
|
H:HOH489
|
4.6
|
52.1
|
1.0
|
C
|
H:GLY366
|
4.8
|
71.7
|
1.0
|
O
|
H:HOH418
|
4.8
|
33.3
|
1.0
|
NE
|
H:ARG367
|
4.8
|
68.9
|
1.0
|
ND1
|
H:HIS363
|
4.9
|
61.8
|
1.0
|
C
|
H:GLY340
|
5.0
|
60.4
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 3ex7
Go back to
Fluorine Binding Sites List in 3ex7
Fluorine binding site 5 out
of 6 in the The Crystal Structure of Ejc in Its Transition State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of The Crystal Structure of Ejc in Its Transition State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F415
b:72.9
occ:1.00
|
F2
|
H:AF3415
|
0.0
|
72.9
|
1.0
|
AL
|
H:AF3415
|
1.8
|
0.4
|
1.0
|
O
|
H:HOH419
|
2.6
|
43.3
|
1.0
|
CB
|
H:ALA219
|
2.9
|
59.3
|
1.0
|
O
|
H:HOH489
|
3.0
|
52.1
|
1.0
|
F3
|
H:AF3415
|
3.1
|
66.6
|
1.0
|
F1
|
H:AF3415
|
3.1
|
52.0
|
1.0
|
O
|
H:HOH421
|
3.1
|
47.8
|
1.0
|
NZ
|
H:LYS88
|
3.5
|
49.7
|
1.0
|
N
|
H:ALA219
|
3.6
|
45.8
|
1.0
|
CA
|
H:ALA219
|
3.8
|
63.9
|
1.0
|
CA
|
H:SER84
|
3.8
|
51.2
|
1.0
|
CB
|
H:SER84
|
3.9
|
52.4
|
1.0
|
CE1
|
H:HIS363
|
4.0
|
58.5
|
1.0
|
ND1
|
H:HIS363
|
4.0
|
61.8
|
1.0
|
O3B
|
H:ADP414
|
4.2
|
52.4
|
1.0
|
O
|
H:SER82
|
4.4
|
55.2
|
1.0
|
N
|
H:SER84
|
4.5
|
52.3
|
1.0
|
O2B
|
H:ADP414
|
4.6
|
42.2
|
1.0
|
N
|
H:GLY85
|
4.7
|
55.6
|
1.0
|
CE
|
H:LYS88
|
4.7
|
64.8
|
1.0
|
O
|
H:HOH491
|
4.7
|
48.8
|
1.0
|
C
|
H:SER218
|
4.8
|
59.0
|
1.0
|
PB
|
H:ADP414
|
4.8
|
49.0
|
1.0
|
O
|
H:GLN83
|
4.8
|
59.2
|
1.0
|
OE2
|
H:GLU188
|
4.8
|
65.6
|
1.0
|
OE1
|
H:GLU188
|
4.8
|
59.5
|
1.0
|
C
|
H:GLN83
|
4.8
|
55.2
|
1.0
|
C
|
H:SER84
|
4.9
|
55.7
|
1.0
|
NH2
|
H:ARG367
|
5.0
|
63.7
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 3ex7
Go back to
Fluorine Binding Sites List in 3ex7
Fluorine binding site 6 out
of 6 in the The Crystal Structure of Ejc in Its Transition State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of The Crystal Structure of Ejc in Its Transition State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F415
b:66.6
occ:1.00
|
F3
|
H:AF3415
|
0.0
|
66.6
|
1.0
|
AL
|
H:AF3415
|
1.8
|
0.4
|
1.0
|
MG
|
H:MG416
|
2.2
|
40.2
|
1.0
|
O3B
|
H:ADP414
|
2.8
|
52.4
|
1.0
|
O
|
H:HOH490
|
3.0
|
41.8
|
1.0
|
O
|
H:HOH421
|
3.0
|
47.8
|
1.0
|
F1
|
H:AF3415
|
3.1
|
52.0
|
1.0
|
O
|
H:HOH491
|
3.1
|
48.8
|
1.0
|
F2
|
H:AF3415
|
3.1
|
72.9
|
1.0
|
O1B
|
H:ADP414
|
3.2
|
45.1
|
1.0
|
O
|
H:HOH492
|
3.2
|
28.3
|
1.0
|
PB
|
H:ADP414
|
3.4
|
49.0
|
1.0
|
OE1
|
H:GLU188
|
3.6
|
59.5
|
1.0
|
CA
|
H:GLY340
|
3.6
|
60.0
|
1.0
|
O
|
H:HOH419
|
3.7
|
43.3
|
1.0
|
O
|
H:HOH489
|
4.0
|
52.1
|
1.0
|
NZ
|
H:LYS88
|
4.1
|
49.7
|
1.0
|
N
|
H:GLY340
|
4.1
|
61.2
|
1.0
|
O2B
|
H:ADP414
|
4.2
|
42.2
|
1.0
|
OG1
|
H:THR89
|
4.4
|
61.1
|
1.0
|
CD
|
H:GLU188
|
4.5
|
60.0
|
1.0
|
O
|
H:GLY340
|
4.5
|
47.8
|
1.0
|
C
|
H:GLY340
|
4.6
|
60.4
|
1.0
|
NH2
|
H:ARG370
|
4.6
|
51.3
|
1.0
|
O3A
|
H:ADP414
|
4.7
|
60.1
|
1.0
|
OE2
|
H:GLU188
|
4.8
|
65.6
|
1.0
|
|
Reference:
K.H.Nielsen,
H.Chamieh,
C.B.Andersen,
F.Fredslund,
K.Hamborg,
H.Le Hir,
G.R.Andersen.
Mechanism of Atp Turnover Inhibition in the Ejc Rna V. 15 67 2009.
ISSN: ISSN 1355-8382
PubMed: 19033377
DOI: 10.1261/RNA.1283109
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