Fluorine in PDB 7pmq: Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3
Enzymatic activity of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3
All present enzymatic activity of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3:
3.6.4.13;
Protein crystallography data
The structure of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3, PDB code: 7pmq
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)
|
49.42 /
3.22
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
159.644,
159.644,
204.682,
90,
90,
90
|
R / Rfree (%)
|
22.8 /
26.4
|
Other elements in 7pmq:
The structure of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3 also contains other interesting chemical elements:
Fluorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Fluorine atom in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3
(pdb code 7pmq). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the
Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3, PDB code: 7pmq:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Fluorine binding site 1 out
of 12 in 7pmq
Go back to
Fluorine Binding Sites List in 7pmq
Fluorine binding site 1 out
of 12 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna 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 Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F501
b:61.0
occ:1.00
|
F1
|
C:BEF501
|
0.0
|
61.0
|
1.0
|
BE
|
C:BEF501
|
1.5
|
61.0
|
1.0
|
MG
|
C:MG502
|
1.9
|
49.4
|
1.0
|
O1B
|
C:ADP500
|
2.2
|
61.4
|
1.0
|
F3
|
C:BEF501
|
2.5
|
61.0
|
1.0
|
F2
|
C:BEF501
|
2.6
|
61.0
|
1.0
|
O3B
|
C:ADP500
|
2.8
|
61.4
|
1.0
|
PB
|
C:ADP500
|
3.0
|
61.4
|
1.0
|
O1A
|
C:ADP500
|
3.2
|
61.4
|
1.0
|
CA
|
C:GLY304
|
3.4
|
59.1
|
1.0
|
O
|
C:GLY304
|
3.7
|
59.0
|
1.0
|
OE2
|
C:GLU154
|
3.8
|
61.9
|
1.0
|
NH2
|
C:ARG334
|
3.8
|
59.8
|
1.0
|
O2B
|
C:ADP500
|
4.0
|
61.4
|
1.0
|
C
|
C:GLY304
|
4.0
|
58.6
|
1.0
|
OE1
|
C:GLU154
|
4.1
|
61.8
|
1.0
|
O3A
|
C:ADP500
|
4.2
|
61.4
|
1.0
|
CE
|
C:LYS53
|
4.2
|
60.4
|
1.0
|
N
|
C:GLY304
|
4.2
|
58.9
|
1.0
|
PA
|
C:ADP500
|
4.3
|
61.4
|
1.0
|
CD
|
C:GLU154
|
4.3
|
62.1
|
1.0
|
NZ
|
C:LYS53
|
4.4
|
60.6
|
1.0
|
OG1
|
C:THR54
|
4.6
|
59.8
|
1.0
|
NH1
|
C:ARG334
|
4.6
|
59.7
|
1.0
|
CZ
|
C:ARG334
|
4.7
|
59.7
|
1.0
|
OD2
|
C:ASP153
|
4.9
|
61.8
|
1.0
|
OD1
|
C:ASP153
|
4.9
|
61.7
|
1.0
|
|
Fluorine binding site 2 out
of 12 in 7pmq
Go back to
Fluorine Binding Sites List in 7pmq
Fluorine binding site 2 out
of 12 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna 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 Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F501
b:61.0
occ:1.00
|
F2
|
C:BEF501
|
0.0
|
61.0
|
1.0
|
BE
|
C:BEF501
|
1.6
|
61.0
|
1.0
|
O1B
|
C:ADP500
|
2.2
|
61.4
|
1.0
|
F3
|
C:BEF501
|
2.5
|
61.0
|
1.0
|
F1
|
C:BEF501
|
2.6
|
61.0
|
1.0
|
NZ
|
C:LYS53
|
2.9
|
60.6
|
1.0
|
CE
|
C:LYS53
|
3.2
|
60.4
|
1.0
|
PB
|
C:ADP500
|
3.3
|
61.4
|
1.0
|
O2B
|
C:ADP500
|
3.4
|
61.4
|
1.0
|
OE2
|
C:GLU154
|
3.5
|
61.9
|
1.0
|
NH2
|
C:ARG334
|
3.7
|
59.8
|
1.0
|
O3B
|
C:ADP500
|
3.9
|
61.4
|
1.0
|
MG
|
C:MG502
|
4.0
|
49.4
|
1.0
|
CA
|
C:THR49
|
4.0
|
60.3
|
1.0
|
N
|
C:GLY50
|
4.1
|
59.8
|
1.0
|
CB
|
C:ALA185
|
4.2
|
60.0
|
1.0
|
O
|
C:LYS48
|
4.2
|
59.7
|
1.0
|
NH2
|
C:ARG331
|
4.5
|
59.9
|
1.0
|
CB
|
C:THR49
|
4.5
|
60.9
|
1.0
|
CD
|
C:LYS53
|
4.5
|
60.6
|
1.0
|
C
|
C:THR49
|
4.6
|
60.5
|
1.0
|
CD
|
C:GLU154
|
4.6
|
62.1
|
1.0
|
CG2
|
C:THR49
|
4.7
|
61.0
|
1.0
|
O3A
|
C:ADP500
|
4.7
|
61.4
|
1.0
|
N
|
C:THR49
|
4.9
|
60.5
|
1.0
|
C
|
C:LYS48
|
4.9
|
60.3
|
1.0
|
CZ
|
C:ARG334
|
5.0
|
59.7
|
1.0
|
CA
|
C:GLY304
|
5.0
|
59.1
|
1.0
|
|
Fluorine binding site 3 out
of 12 in 7pmq
Go back to
Fluorine Binding Sites List in 7pmq
Fluorine binding site 3 out
of 12 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna 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 Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F501
b:61.0
occ:1.00
|
F3
|
C:BEF501
|
0.0
|
61.0
|
1.0
|
BE
|
C:BEF501
|
1.5
|
61.0
|
1.0
|
F2
|
C:BEF501
|
2.5
|
61.0
|
1.0
|
NH2
|
C:ARG334
|
2.5
|
59.8
|
1.0
|
F1
|
C:BEF501
|
2.5
|
61.0
|
1.0
|
NH2
|
C:ARG331
|
2.6
|
59.9
|
1.0
|
O1B
|
C:ADP500
|
2.7
|
61.4
|
1.0
|
NH1
|
C:ARG331
|
3.1
|
59.3
|
1.0
|
CA
|
C:GLY304
|
3.1
|
59.1
|
1.0
|
N
|
C:GLY304
|
3.2
|
58.9
|
1.0
|
CZ
|
C:ARG331
|
3.3
|
59.4
|
1.0
|
CZ
|
C:ARG334
|
3.6
|
59.7
|
1.0
|
C
|
C:GLY304
|
3.7
|
58.6
|
1.0
|
O
|
C:GLY304
|
3.9
|
59.0
|
1.0
|
OE2
|
C:GLU154
|
4.0
|
61.9
|
1.0
|
NH1
|
C:ARG334
|
4.1
|
59.7
|
1.0
|
PB
|
C:ADP500
|
4.3
|
61.4
|
1.0
|
MG
|
C:MG502
|
4.3
|
49.4
|
1.0
|
C
|
C:ARG303
|
4.4
|
58.4
|
1.0
|
NE
|
C:ARG334
|
4.5
|
59.8
|
1.0
|
N
|
C:LEU305
|
4.6
|
57.4
|
1.0
|
NE
|
C:ARG331
|
4.6
|
59.2
|
1.0
|
N
|
C:GLY50
|
4.7
|
59.8
|
1.0
|
O1A
|
C:ADP500
|
4.7
|
61.4
|
1.0
|
O
|
C:LEU305
|
4.8
|
57.4
|
1.0
|
CB
|
C:THR49
|
4.8
|
60.9
|
1.0
|
CD
|
C:GLU154
|
4.8
|
62.1
|
1.0
|
O3B
|
C:ADP500
|
4.9
|
61.4
|
1.0
|
CA
|
C:THR49
|
4.9
|
60.3
|
1.0
|
|
Fluorine binding site 4 out
of 12 in 7pmq
Go back to
Fluorine Binding Sites List in 7pmq
Fluorine binding site 4 out
of 12 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna 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 Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:58.5
occ:1.00
|
F1
|
A:BEF501
|
0.0
|
58.5
|
1.0
|
BE
|
A:BEF501
|
1.5
|
58.5
|
1.0
|
MG
|
A:MG502
|
2.0
|
46.0
|
1.0
|
O3B
|
A:ADP500
|
2.5
|
57.9
|
1.0
|
F3
|
A:BEF501
|
2.5
|
58.5
|
1.0
|
O1B
|
A:ADP500
|
2.6
|
57.9
|
1.0
|
F2
|
A:BEF501
|
2.6
|
58.5
|
1.0
|
PB
|
A:ADP500
|
2.9
|
57.9
|
1.0
|
O1A
|
A:ADP500
|
3.0
|
57.9
|
1.0
|
O3A
|
A:ADP500
|
3.5
|
57.9
|
1.0
|
NH2
|
A:ARG334
|
3.6
|
58.5
|
1.0
|
CA
|
A:GLY304
|
3.6
|
57.3
|
1.0
|
O
|
A:GLY304
|
3.7
|
57.1
|
1.0
|
PA
|
A:ADP500
|
3.9
|
57.9
|
1.0
|
OE2
|
A:GLU154
|
4.1
|
59.6
|
1.0
|
C
|
A:GLY304
|
4.2
|
56.8
|
1.0
|
OG1
|
A:THR54
|
4.2
|
55.0
|
1.0
|
O2B
|
A:ADP500
|
4.3
|
57.9
|
1.0
|
OE1
|
A:GLU154
|
4.4
|
58.3
|
1.0
|
N
|
A:GLY304
|
4.5
|
57.1
|
1.0
|
CZ
|
A:ARG334
|
4.6
|
58.2
|
1.0
|
O2A
|
A:ADP500
|
4.6
|
57.9
|
1.0
|
NH1
|
A:ARG334
|
4.6
|
58.3
|
1.0
|
OD2
|
A:ASP153
|
4.6
|
56.3
|
1.0
|
CD
|
A:GLU154
|
4.7
|
59.1
|
1.0
|
NZ
|
A:LYS53
|
4.7
|
56.9
|
1.0
|
OD1
|
A:ASP153
|
4.8
|
56.3
|
1.0
|
NH1
|
A:ARG331
|
5.0
|
58.1
|
1.0
|
CE
|
A:LYS53
|
5.0
|
56.7
|
1.0
|
|
Fluorine binding site 5 out
of 12 in 7pmq
Go back to
Fluorine Binding Sites List in 7pmq
Fluorine binding site 5 out
of 12 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna 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 Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:58.5
occ:1.00
|
F2
|
A:BEF501
|
0.0
|
58.5
|
1.0
|
BE
|
A:BEF501
|
1.6
|
58.5
|
1.0
|
NZ
|
A:LYS53
|
2.4
|
56.9
|
1.0
|
F3
|
A:BEF501
|
2.5
|
58.5
|
1.0
|
F1
|
A:BEF501
|
2.6
|
58.5
|
1.0
|
O1B
|
A:ADP500
|
2.6
|
57.9
|
1.0
|
MG
|
A:MG502
|
2.8
|
46.0
|
1.0
|
OE2
|
A:GLU154
|
2.9
|
59.6
|
1.0
|
CE
|
A:LYS53
|
3.1
|
56.7
|
1.0
|
O3B
|
A:ADP500
|
3.3
|
57.9
|
1.0
|
PB
|
A:ADP500
|
3.5
|
57.9
|
1.0
|
CD
|
A:GLU154
|
3.7
|
59.1
|
1.0
|
OE1
|
A:GLU154
|
3.9
|
58.3
|
1.0
|
CD
|
A:LYS53
|
4.1
|
55.9
|
1.0
|
OD1
|
A:ASP153
|
4.1
|
56.3
|
1.0
|
O2B
|
A:ADP500
|
4.3
|
57.9
|
1.0
|
N
|
A:ALA185
|
4.6
|
55.1
|
1.0
|
CB
|
A:ALA185
|
4.7
|
57.0
|
1.0
|
CB
|
A:LYS53
|
4.7
|
54.8
|
1.0
|
O3A
|
A:ADP500
|
4.9
|
57.9
|
1.0
|
CG
|
A:LYS53
|
4.9
|
55.6
|
1.0
|
NH2
|
A:ARG334
|
4.9
|
58.5
|
1.0
|
CA
|
A:GLY304
|
5.0
|
57.3
|
1.0
|
CG
|
A:GLU154
|
5.0
|
59.6
|
1.0
|
|
Fluorine binding site 6 out
of 12 in 7pmq
Go back to
Fluorine Binding Sites List in 7pmq
Fluorine binding site 6 out
of 12 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna 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 Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:58.5
occ:1.00
|
F3
|
A:BEF501
|
0.0
|
58.5
|
1.0
|
BE
|
A:BEF501
|
1.5
|
58.5
|
1.0
|
O1B
|
A:ADP500
|
1.8
|
57.9
|
1.0
|
F2
|
A:BEF501
|
2.5
|
58.5
|
1.0
|
F1
|
A:BEF501
|
2.5
|
58.5
|
1.0
|
NH2
|
A:ARG334
|
2.6
|
58.5
|
1.0
|
PB
|
A:ADP500
|
3.3
|
57.9
|
1.0
|
NH2
|
A:ARG331
|
3.4
|
58.7
|
1.0
|
N
|
A:GLY50
|
3.7
|
56.8
|
1.0
|
OE2
|
A:GLU154
|
3.8
|
59.6
|
1.0
|
NZ
|
A:LYS53
|
3.8
|
56.9
|
1.0
|
CZ
|
A:ARG334
|
3.9
|
58.2
|
1.0
|
NH1
|
A:ARG331
|
3.9
|
58.1
|
1.0
|
O3B
|
A:ADP500
|
4.0
|
57.9
|
1.0
|
O3A
|
A:ADP500
|
4.0
|
57.9
|
1.0
|
CA
|
A:THR49
|
4.0
|
57.6
|
1.0
|
MG
|
A:MG502
|
4.1
|
46.0
|
1.0
|
CZ
|
A:ARG331
|
4.2
|
58.2
|
1.0
|
CA
|
A:GLY304
|
4.2
|
57.3
|
1.0
|
C
|
A:THR49
|
4.3
|
58.0
|
1.0
|
N
|
A:GLY304
|
4.4
|
57.1
|
1.0
|
CE
|
A:LYS53
|
4.4
|
56.7
|
1.0
|
O2B
|
A:ADP500
|
4.4
|
57.9
|
1.0
|
CB
|
A:THR49
|
4.4
|
59.0
|
1.0
|
CA
|
A:GLY50
|
4.6
|
57.3
|
1.0
|
NH1
|
A:ARG334
|
4.7
|
58.3
|
1.0
|
NE
|
A:ARG334
|
4.8
|
58.1
|
1.0
|
CD
|
A:GLU154
|
4.9
|
59.1
|
1.0
|
O
|
A:GLY304
|
4.9
|
57.1
|
1.0
|
C
|
A:GLY304
|
4.9
|
56.8
|
1.0
|
O1A
|
A:ADP500
|
4.9
|
57.9
|
1.0
|
|
Fluorine binding site 7 out
of 12 in 7pmq
Go back to
Fluorine Binding Sites List in 7pmq
Fluorine binding site 7 out
of 12 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:68.8
occ:1.00
|
F1
|
B:BEF501
|
0.0
|
68.8
|
1.0
|
BE
|
B:BEF501
|
1.5
|
68.8
|
1.0
|
MG
|
B:MG502
|
1.9
|
61.5
|
1.0
|
O2B
|
B:ADP500
|
2.4
|
70.0
|
1.0
|
F3
|
B:BEF501
|
2.5
|
68.8
|
1.0
|
F2
|
B:BEF501
|
2.6
|
68.8
|
1.0
|
O2A
|
B:ADP500
|
3.0
|
70.0
|
1.0
|
CA
|
B:GLY304
|
3.2
|
66.0
|
1.0
|
O3B
|
B:ADP500
|
3.2
|
70.0
|
1.0
|
O
|
B:GLY304
|
3.3
|
65.0
|
1.0
|
PB
|
B:ADP500
|
3.3
|
70.0
|
1.0
|
NH2
|
B:ARG334
|
3.6
|
64.3
|
1.0
|
C
|
B:GLY304
|
3.6
|
64.6
|
1.0
|
OE2
|
B:GLU154
|
3.8
|
70.8
|
1.0
|
N
|
B:GLY304
|
4.1
|
65.6
|
1.0
|
OE1
|
B:GLU154
|
4.1
|
70.9
|
1.0
|
O3A
|
B:ADP500
|
4.2
|
70.0
|
1.0
|
PA
|
B:ADP500
|
4.2
|
70.0
|
1.0
|
CD
|
B:GLU154
|
4.4
|
71.0
|
1.0
|
OD2
|
B:ASP153
|
4.4
|
73.4
|
1.0
|
O1B
|
B:ADP500
|
4.5
|
70.0
|
1.0
|
NH1
|
B:ARG331
|
4.6
|
63.6
|
1.0
|
OG1
|
B:THR54
|
4.6
|
71.0
|
1.0
|
CZ
|
B:ARG334
|
4.8
|
62.8
|
1.0
|
CD1
|
B:LEU83
|
4.8
|
68.8
|
1.0
|
OD1
|
B:ASP153
|
4.9
|
74.0
|
1.0
|
N
|
B:LEU305
|
4.9
|
65.3
|
1.0
|
NE2
|
B:GLN86
|
4.9
|
67.3
|
1.0
|
|
Fluorine binding site 8 out
of 12 in 7pmq
Go back to
Fluorine Binding Sites List in 7pmq
Fluorine binding site 8 out
of 12 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:68.8
occ:1.00
|
F2
|
B:BEF501
|
0.0
|
68.8
|
1.0
|
BE
|
B:BEF501
|
1.6
|
68.8
|
1.0
|
MG
|
B:MG502
|
2.5
|
61.5
|
1.0
|
F3
|
B:BEF501
|
2.5
|
68.8
|
1.0
|
F1
|
B:BEF501
|
2.6
|
68.8
|
1.0
|
O2B
|
B:ADP500
|
2.6
|
70.0
|
1.0
|
O3B
|
B:ADP500
|
2.7
|
70.0
|
1.0
|
NZ
|
B:LYS53
|
3.1
|
70.7
|
1.0
|
PB
|
B:ADP500
|
3.1
|
70.0
|
1.0
|
OE2
|
B:GLU154
|
3.1
|
70.8
|
1.0
|
O1B
|
B:ADP500
|
3.5
|
70.0
|
1.0
|
OD1
|
B:ASP153
|
3.7
|
74.0
|
1.0
|
CD
|
B:LYS53
|
3.8
|
71.3
|
1.0
|
CD
|
B:GLU154
|
3.9
|
71.0
|
1.0
|
CE
|
B:LYS53
|
3.9
|
71.2
|
1.0
|
OE1
|
B:GLU154
|
3.9
|
70.9
|
1.0
|
CB
|
B:LYS53
|
4.4
|
71.1
|
1.0
|
OD2
|
B:ASP153
|
4.4
|
73.4
|
1.0
|
CG
|
B:ASP153
|
4.5
|
74.0
|
1.0
|
CG
|
B:LYS53
|
4.5
|
71.4
|
1.0
|
O2A
|
B:ADP500
|
4.5
|
70.0
|
1.0
|
O3A
|
B:ADP500
|
4.6
|
70.0
|
1.0
|
NH2
|
B:ARG334
|
4.9
|
64.3
|
1.0
|
|
Fluorine binding site 9 out
of 12 in 7pmq
Go back to
Fluorine Binding Sites List in 7pmq
Fluorine binding site 9 out
of 12 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 9 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:68.8
occ:1.00
|
F3
|
B:BEF501
|
0.0
|
68.8
|
1.0
|
BE
|
B:BEF501
|
1.5
|
68.8
|
1.0
|
O2B
|
B:ADP500
|
2.2
|
70.0
|
1.0
|
F2
|
B:BEF501
|
2.5
|
68.8
|
1.0
|
F1
|
B:BEF501
|
2.5
|
68.8
|
1.0
|
OE2
|
B:GLU154
|
3.0
|
70.8
|
1.0
|
NH2
|
B:ARG334
|
3.1
|
64.3
|
1.0
|
NH2
|
B:ARG331
|
3.5
|
64.8
|
1.0
|
PB
|
B:ADP500
|
3.7
|
70.0
|
1.0
|
NZ
|
B:LYS53
|
3.9
|
70.7
|
1.0
|
MG
|
B:MG502
|
3.9
|
61.5
|
1.0
|
NH1
|
B:ARG331
|
4.0
|
63.6
|
1.0
|
CA
|
B:GLY304
|
4.0
|
66.0
|
1.0
|
N
|
B:GLY304
|
4.1
|
65.6
|
1.0
|
O1B
|
B:ADP500
|
4.2
|
70.0
|
1.0
|
CD
|
B:GLU154
|
4.2
|
71.0
|
1.0
|
CZ
|
B:ARG331
|
4.2
|
63.5
|
1.0
|
N
|
B:GLY50
|
4.2
|
68.0
|
1.0
|
O3B
|
B:ADP500
|
4.2
|
70.0
|
1.0
|
CZ
|
B:ARG334
|
4.3
|
62.8
|
1.0
|
CA
|
B:THR49
|
4.4
|
68.1
|
1.0
|
CB
|
B:THR49
|
4.6
|
68.2
|
1.0
|
NH1
|
B:ARG334
|
4.6
|
61.8
|
1.0
|
OE1
|
B:GLU154
|
4.7
|
70.9
|
1.0
|
ND1
|
B:HIS327
|
4.7
|
69.7
|
1.0
|
O3A
|
B:ADP500
|
4.8
|
70.0
|
1.0
|
C
|
B:GLY304
|
4.8
|
64.6
|
1.0
|
C
|
B:THR49
|
4.8
|
67.8
|
1.0
|
CE1
|
B:HIS327
|
4.8
|
71.8
|
1.0
|
O
|
B:GLY304
|
4.9
|
65.0
|
1.0
|
O2A
|
B:ADP500
|
5.0
|
70.0
|
1.0
|
|
Fluorine binding site 10 out
of 12 in 7pmq
Go back to
Fluorine Binding Sites List in 7pmq
Fluorine binding site 10 out
of 12 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 10 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F501
b:86.5
occ:1.00
|
F1
|
D:BEF501
|
0.0
|
86.5
|
1.0
|
BE
|
D:BEF501
|
1.5
|
86.5
|
1.0
|
MG
|
D:MG502
|
2.0
|
82.7
|
1.0
|
O2B
|
D:ADP500
|
2.4
|
88.1
|
1.0
|
F3
|
D:BEF501
|
2.5
|
86.5
|
1.0
|
F2
|
D:BEF501
|
2.6
|
86.5
|
1.0
|
O2A
|
D:ADP500
|
3.0
|
88.1
|
1.0
|
O3B
|
D:ADP500
|
3.2
|
88.1
|
1.0
|
CA
|
D:GLY304
|
3.3
|
80.8
|
1.0
|
O
|
D:GLY304
|
3.3
|
79.9
|
1.0
|
PB
|
D:ADP500
|
3.4
|
88.1
|
1.0
|
NH2
|
D:ARG334
|
3.7
|
78.2
|
1.0
|
C
|
D:GLY304
|
3.7
|
79.2
|
1.0
|
O3A
|
D:ADP500
|
4.1
|
88.1
|
1.0
|
OE2
|
D:GLU154
|
4.2
|
88.2
|
1.0
|
PA
|
D:ADP500
|
4.2
|
88.1
|
1.0
|
N
|
D:GLY304
|
4.2
|
80.1
|
1.0
|
OG1
|
D:THR54
|
4.4
|
89.0
|
1.0
|
NH1
|
D:ARG331
|
4.4
|
77.4
|
1.0
|
OE1
|
D:GLU154
|
4.4
|
87.6
|
1.0
|
OD2
|
D:ASP153
|
4.4
|
88.2
|
1.0
|
NH1
|
D:ARG334
|
4.5
|
76.8
|
1.0
|
CZ
|
D:ARG334
|
4.6
|
76.8
|
1.0
|
O1B
|
D:ADP500
|
4.6
|
88.1
|
1.0
|
CD
|
D:GLU154
|
4.7
|
88.1
|
1.0
|
NE2
|
D:GLN86
|
4.8
|
79.2
|
1.0
|
CD1
|
D:LEU83
|
5.0
|
79.7
|
1.0
|
|
Reference:
J.P.Wurm,
J.P.Wurm.
N/A N/A.
Page generated: Fri Aug 2 11:08:16 2024
|