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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:

Magnesium (Mg) 4 atoms

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

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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

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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

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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: Tue Jul 15 22:50:31 2025

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