Fluorine in PDB 7pmm: Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3
Enzymatic activity of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3
All present enzymatic activity of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3:
3.6.4.13;
Protein crystallography data
The structure of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3, PDB code: 7pmm
was solved by
J.P.Wurm,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.39 /
3.00
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
169.69,
169.69,
111.99,
90,
90,
90
|
R / Rfree (%)
|
19.7 /
22.5
|
Other elements in 7pmm:
The structure of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3
(pdb code 7pmm). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3, PDB code: 7pmm:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 7pmm
Go back to
Fluorine Binding Sites List in 7pmm
Fluorine binding site 1 out
of 6 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:66.2
occ:1.00
|
F1
|
A:BEF501
|
0.0
|
66.2
|
1.0
|
BE
|
A:BEF501
|
1.5
|
63.1
|
1.0
|
NH2
|
A:ARG331
|
2.5
|
61.0
|
1.0
|
F3
|
A:BEF501
|
2.6
|
65.6
|
1.0
|
NH1
|
A:ARG334
|
2.6
|
57.2
|
1.0
|
F2
|
A:BEF501
|
2.6
|
63.3
|
1.0
|
O1B
|
A:ADP500
|
2.7
|
63.1
|
1.0
|
NH1
|
A:ARG331
|
3.0
|
58.1
|
1.0
|
CZ
|
A:ARG331
|
3.2
|
57.0
|
1.0
|
CZ
|
A:ARG334
|
3.4
|
62.5
|
1.0
|
NH2
|
A:ARG334
|
3.4
|
63.4
|
1.0
|
N
|
A:GLY50
|
3.7
|
60.4
|
1.0
|
CG2
|
A:THR49
|
3.7
|
52.0
|
1.0
|
CB
|
A:THR49
|
3.8
|
59.4
|
1.0
|
CA
|
A:GLY304
|
3.9
|
63.7
|
1.0
|
N
|
A:GLY304
|
3.9
|
62.8
|
1.0
|
CA
|
A:THR49
|
4.1
|
60.2
|
1.0
|
PB
|
A:ADP500
|
4.2
|
63.1
|
1.0
|
C
|
A:GLY304
|
4.3
|
59.4
|
1.0
|
C
|
A:THR49
|
4.4
|
63.5
|
1.0
|
O
|
A:GLY304
|
4.4
|
66.5
|
1.0
|
NE
|
A:ARG331
|
4.5
|
64.2
|
1.0
|
MG
|
A:MG502
|
4.5
|
63.1
|
1.0
|
O
|
A:HOH601
|
4.5
|
81.0
|
1.0
|
CA
|
A:GLY50
|
4.5
|
63.0
|
1.0
|
O
|
A:GLY330
|
4.7
|
72.7
|
1.0
|
NE
|
A:ARG334
|
4.7
|
61.2
|
1.0
|
O3B
|
A:ADP500
|
4.7
|
63.1
|
1.0
|
O2B
|
A:ADP500
|
5.0
|
63.1
|
1.0
|
OE2
|
A:GLU154
|
5.0
|
73.5
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 7pmm
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Fluorine Binding Sites List in 7pmm
Fluorine binding site 2 out
of 6 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:63.3
occ:1.00
|
F2
|
A:BEF501
|
0.0
|
63.3
|
1.0
|
BE
|
A:BEF501
|
1.6
|
63.1
|
1.0
|
MG
|
A:MG502
|
2.0
|
63.1
|
1.0
|
F3
|
A:BEF501
|
2.6
|
65.6
|
1.0
|
F1
|
A:BEF501
|
2.6
|
66.2
|
1.0
|
O1B
|
A:ADP500
|
2.7
|
63.1
|
1.0
|
O
|
A:HOH603
|
2.8
|
75.2
|
1.0
|
O
|
A:HOH604
|
2.9
|
64.1
|
1.0
|
O
|
A:HOH601
|
2.9
|
81.0
|
1.0
|
O3B
|
A:ADP500
|
2.9
|
63.1
|
1.0
|
OE2
|
A:GLU154
|
3.3
|
73.5
|
1.0
|
CA
|
A:GLY304
|
3.3
|
63.7
|
1.0
|
PB
|
A:ADP500
|
3.4
|
63.1
|
1.0
|
N
|
A:GLY304
|
3.9
|
62.8
|
1.0
|
O
|
A:GLY304
|
4.1
|
66.5
|
1.0
|
O
|
A:HOH602
|
4.1
|
72.7
|
1.0
|
O1A
|
A:ADP500
|
4.1
|
76.6
|
1.0
|
C
|
A:GLY304
|
4.1
|
59.4
|
1.0
|
O2B
|
A:ADP500
|
4.2
|
63.1
|
1.0
|
NZ
|
A:LYS53
|
4.3
|
60.2
|
1.0
|
NH2
|
A:ARG334
|
4.3
|
63.4
|
1.0
|
CD
|
A:GLU154
|
4.4
|
71.2
|
1.0
|
NH2
|
A:ARG331
|
4.6
|
61.0
|
1.0
|
NH1
|
A:ARG331
|
4.7
|
58.1
|
1.0
|
O3A
|
A:ADP500
|
4.7
|
66.6
|
1.0
|
NH1
|
A:ARG334
|
4.7
|
57.2
|
1.0
|
OE1
|
A:GLU154
|
5.0
|
80.0
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 7pmm
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Fluorine Binding Sites List in 7pmm
Fluorine binding site 3 out
of 6 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:65.6
occ:1.00
|
F3
|
A:BEF501
|
0.0
|
65.6
|
1.0
|
BE
|
A:BEF501
|
1.5
|
63.1
|
1.0
|
F2
|
A:BEF501
|
2.6
|
63.3
|
1.0
|
F1
|
A:BEF501
|
2.6
|
66.2
|
1.0
|
NZ
|
A:LYS53
|
2.7
|
60.2
|
1.0
|
O1B
|
A:ADP500
|
2.7
|
63.1
|
1.0
|
CG2
|
A:THR49
|
3.3
|
52.0
|
1.0
|
CA
|
A:THR49
|
3.3
|
60.2
|
1.0
|
O2B
|
A:ADP500
|
3.7
|
63.1
|
1.0
|
CB
|
A:THR49
|
3.7
|
59.4
|
1.0
|
PB
|
A:ADP500
|
3.7
|
63.1
|
1.0
|
N
|
A:GLY50
|
3.8
|
60.4
|
1.0
|
O
|
A:HOH604
|
4.0
|
64.1
|
1.0
|
CE
|
A:LYS53
|
4.0
|
61.1
|
1.0
|
CB
|
A:ALA185
|
4.0
|
55.9
|
1.0
|
C
|
A:THR49
|
4.1
|
63.5
|
1.0
|
O
|
A:LYS48
|
4.1
|
60.5
|
1.0
|
O3B
|
A:ADP500
|
4.1
|
63.1
|
1.0
|
MG
|
A:MG502
|
4.2
|
63.1
|
1.0
|
N
|
A:THR49
|
4.2
|
59.0
|
1.0
|
NH2
|
A:ARG331
|
4.4
|
61.0
|
1.0
|
C
|
A:LYS48
|
4.5
|
59.4
|
1.0
|
OE2
|
A:GLU154
|
4.6
|
73.5
|
1.0
|
NH1
|
A:ARG334
|
4.8
|
57.2
|
1.0
|
CD
|
A:LYS53
|
4.8
|
58.4
|
1.0
|
N
|
A:ALA185
|
5.0
|
59.1
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 7pmm
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Fluorine Binding Sites List in 7pmm
Fluorine binding site 4 out
of 6 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:92.2
occ:1.00
|
F1
|
B:BEF501
|
0.0
|
92.2
|
1.0
|
BE
|
B:BEF501
|
1.5
|
92.7
|
1.0
|
F3
|
B:BEF501
|
2.6
|
93.6
|
1.0
|
F2
|
B:BEF501
|
2.6
|
95.3
|
1.0
|
O2B
|
B:ADP500
|
2.7
|
88.6
|
1.0
|
NZ
|
B:LYS53
|
2.9
|
82.1
|
1.0
|
CA
|
B:THR49
|
3.3
|
90.0
|
1.0
|
CE
|
B:LYS53
|
3.4
|
84.7
|
1.0
|
CG2
|
B:THR49
|
3.4
|
92.0
|
1.0
|
CB
|
B:ALA185
|
3.7
|
78.0
|
1.0
|
CB
|
B:THR49
|
3.7
|
91.4
|
1.0
|
PB
|
B:ADP500
|
3.9
|
87.7
|
1.0
|
N
|
B:THR49
|
4.0
|
91.8
|
1.0
|
O
|
B:HOH604
|
4.1
|
85.6
|
1.0
|
O
|
B:LYS48
|
4.2
|
91.1
|
1.0
|
N
|
B:GLY50
|
4.2
|
100.0
|
1.0
|
NH2
|
B:ARG331
|
4.3
|
97.2
|
1.0
|
C
|
B:THR49
|
4.3
|
97.1
|
1.0
|
O1B
|
B:ADP500
|
4.3
|
85.3
|
1.0
|
MG
|
B:MG502
|
4.3
|
90.5
|
1.0
|
O3B
|
B:ADP500
|
4.3
|
90.8
|
1.0
|
C
|
B:LYS48
|
4.4
|
91.5
|
1.0
|
OE2
|
B:GLU154
|
4.6
|
92.2
|
1.0
|
O
|
B:ALA47
|
4.6
|
85.9
|
1.0
|
N
|
B:ALA185
|
4.6
|
80.1
|
1.0
|
CA
|
B:ALA185
|
4.7
|
81.7
|
1.0
|
ND1
|
B:HIS327
|
4.8
|
93.0
|
1.0
|
CE1
|
B:HIS327
|
4.8
|
89.0
|
1.0
|
NH1
|
B:ARG334
|
4.9
|
96.6
|
1.0
|
CD
|
B:LYS53
|
4.9
|
78.1
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 7pmm
Go back to
Fluorine Binding Sites List in 7pmm
Fluorine binding site 5 out
of 6 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:95.3
occ:1.00
|
F2
|
B:BEF501
|
0.0
|
95.3
|
1.0
|
BE
|
B:BEF501
|
1.6
|
92.7
|
1.0
|
MG
|
B:MG502
|
2.0
|
90.5
|
1.0
|
F3
|
B:BEF501
|
2.6
|
93.6
|
1.0
|
F1
|
B:BEF501
|
2.6
|
92.2
|
1.0
|
O2B
|
B:ADP500
|
2.7
|
88.6
|
1.0
|
O
|
B:HOH602
|
2.9
|
96.7
|
1.0
|
O
|
B:HOH603
|
2.9
|
97.8
|
1.0
|
O
|
B:HOH604
|
2.9
|
85.6
|
1.0
|
O3B
|
B:ADP500
|
2.9
|
90.8
|
1.0
|
PB
|
B:ADP500
|
3.3
|
87.7
|
1.0
|
OE2
|
B:GLU154
|
3.5
|
92.2
|
1.0
|
CA
|
B:GLY304
|
3.5
|
92.7
|
1.0
|
N
|
B:GLY304
|
4.0
|
95.1
|
1.0
|
O
|
B:HOH601
|
4.1
|
101.0
|
1.0
|
O
|
B:GLY304
|
4.1
|
102.0
|
1.0
|
C
|
B:GLY304
|
4.2
|
97.8
|
1.0
|
NH2
|
B:ARG334
|
4.3
|
97.1
|
1.0
|
CE
|
B:LYS53
|
4.3
|
84.7
|
1.0
|
O2A
|
B:ADP500
|
4.3
|
101.3
|
1.0
|
O1B
|
B:ADP500
|
4.4
|
85.3
|
1.0
|
NZ
|
B:LYS53
|
4.4
|
82.1
|
1.0
|
O3A
|
B:ADP500
|
4.5
|
101.2
|
1.0
|
NH2
|
B:ARG331
|
4.5
|
97.2
|
1.0
|
NH1
|
B:ARG331
|
4.5
|
100.2
|
1.0
|
CD
|
B:GLU154
|
4.6
|
88.8
|
1.0
|
NH1
|
B:ARG334
|
4.8
|
96.6
|
1.0
|
OD2
|
B:ASP153
|
4.9
|
106.6
|
1.0
|
OD1
|
B:ASP153
|
4.9
|
91.0
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 7pmm
Go back to
Fluorine Binding Sites List in 7pmm
Fluorine binding site 6 out
of 6 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:93.6
occ:1.00
|
F3
|
B:BEF501
|
0.0
|
93.6
|
1.0
|
BE
|
B:BEF501
|
1.5
|
92.7
|
1.0
|
F2
|
B:BEF501
|
2.6
|
95.3
|
1.0
|
F1
|
B:BEF501
|
2.6
|
92.2
|
1.0
|
NH1
|
B:ARG334
|
2.6
|
96.6
|
1.0
|
O2B
|
B:ADP500
|
2.7
|
88.6
|
1.0
|
NH2
|
B:ARG331
|
2.7
|
97.2
|
1.0
|
NH1
|
B:ARG331
|
3.0
|
100.2
|
1.0
|
CZ
|
B:ARG331
|
3.2
|
99.4
|
1.0
|
NH2
|
B:ARG334
|
3.3
|
97.1
|
1.0
|
CZ
|
B:ARG334
|
3.4
|
99.9
|
1.0
|
CB
|
B:THR49
|
3.5
|
91.4
|
1.0
|
N
|
B:GLY50
|
3.7
|
100.0
|
1.0
|
CG2
|
B:THR49
|
3.7
|
92.0
|
1.0
|
CA
|
B:THR49
|
3.8
|
90.0
|
1.0
|
N
|
B:GLY304
|
4.1
|
95.1
|
1.0
|
PB
|
B:ADP500
|
4.1
|
87.7
|
1.0
|
CA
|
B:GLY304
|
4.1
|
92.7
|
1.0
|
C
|
B:THR49
|
4.3
|
97.1
|
1.0
|
O
|
B:HOH603
|
4.4
|
97.8
|
1.0
|
MG
|
B:MG502
|
4.4
|
90.5
|
1.0
|
O
|
B:GLY304
|
4.5
|
102.0
|
1.0
|
NE
|
B:ARG331
|
4.5
|
99.6
|
1.0
|
C
|
B:GLY304
|
4.5
|
97.8
|
1.0
|
O3B
|
B:ADP500
|
4.6
|
90.8
|
1.0
|
NE
|
B:ARG334
|
4.7
|
104.5
|
1.0
|
O3A
|
B:ADP500
|
4.8
|
101.2
|
1.0
|
O
|
B:GLY330
|
4.8
|
101.4
|
1.0
|
CA
|
B:GLY50
|
4.8
|
98.3
|
1.0
|
OG1
|
B:THR49
|
4.8
|
101.7
|
1.0
|
OE2
|
B:GLU154
|
5.0
|
92.2
|
1.0
|
|
Reference:
J.P.Wurm,
J.P.Wurm.
N/A N/A.
Page generated: Fri Aug 2 11:08:16 2024
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