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Fluorine in PDB 7pli: Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3

Enzymatic activity of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3

All present enzymatic activity of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3:
3.6.4.13;

Protein crystallography data

The structure of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3, PDB code: 7pli 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) 56.88 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.643, 121.599, 122.417, 97.16, 92.43, 103.44
R / Rfree (%) 21.3 / 24.7

Other elements in 7pli:

The structure of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3 also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3 (pdb code 7pli). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3, PDB code: 7pli:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 7pli

Go back to Fluorine Binding Sites List in 7pli
Fluorine binding site 1 out of 18 in the Dead-Box Helicase Dbpa Bound to Single Stranded 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 Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:40.6
occ:1.00
 F1 A:BEF501 0.0 40.6 1.0
BE A:BEF501 1.5 41.2 1.0
O2B A:ADP500 2.3 42.6 1.0
NH1 A:ARG334 2.5 38.9 1.0
F3 A:BEF501 2.5 41.2 1.0
F2 A:BEF501 2.6 37.1 1.0
NH2 A:ARG334 2.9 40.9 1.0
CZ A:ARG334 3.1 41.6 1.0
NH1 A:ARG331 3.1 38.9 1.0
NH2 A:ARG331 3.2 40.6 1.0
N A:GLY50 3.5 39.8 1.0
CZ A:ARG331 3.6 43.5 1.0
PB A:ADP500 3.8 38.6 1.0
CA A:GLY304 3.8 39.6 1.0
CB A:THR49 3.8 42.0 1.0
N A:GLY304 4.0 43.5 1.0
O A:HOH601 4.1 40.2 1.0
CA A:THR49 4.1 42.6 1.0
CG2 A:THR49 4.2 42.2 1.0
C A:GLY304 4.3 39.5 1.0
C A:THR49 4.3 42.4 1.0
O A:GLY304 4.3 39.7 1.0
O1B A:ADP500 4.3 36.5 1.0
CA A:GLY50 4.4 41.5 1.0
NE A:ARG334 4.4 42.1 1.0
O3A A:ADP500 4.5 40.2 1.0
MG A:MG502 4.5 40.0 1.0
O2A A:ADP500 4.6 48.2 1.0
O A:GLY330 4.7 42.2 1.0
O3B A:ADP500 4.8 41.8 1.0
NE A:ARG331 4.9 42.1 1.0

Fluorine binding site 2 out of 18 in 7pli

Go back to Fluorine Binding Sites List in 7pli
Fluorine binding site 2 out of 18 in the Dead-Box Helicase Dbpa Bound to Single Stranded 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 Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:37.1
occ:1.00
 F2 A:BEF501 0.0 37.1 1.0
BE A:BEF501 1.6 41.2 1.0
MG A:MG502 2.1 40.0 1.0
F3 A:BEF501 2.5 41.2 1.0
O2B A:ADP500 2.5 42.6 1.0
F1 A:BEF501 2.6 40.6 1.0
O1B A:ADP500 2.7 36.5 1.0
O A:HOH601 2.8 40.2 1.0
O A:HOH604 2.8 37.7 1.0
PB A:ADP500 3.1 38.6 1.0
O A:HOH602 3.1 41.4 1.0
OE2 A:GLU154 3.3 45.7 1.0
CA A:GLY304 3.4 39.6 1.0
O2A A:ADP500 3.9 48.2 1.0
N A:GLY304 4.0 43.5 1.0
NH2 A:ARG334 4.1 40.9 1.0
O A:HOH603 4.2 38.2 1.0
O A:GLY304 4.2 39.7 1.0
O3B A:ADP500 4.2 41.8 1.0
O3A A:ADP500 4.3 40.2 1.0
C A:GLY304 4.3 39.5 1.0
NZ A:LYS53 4.4 39.5 1.0
CD A:GLU154 4.5 46.0 1.0
CE A:LYS53 4.5 42.6 1.0
PA A:ADP500 4.7 36.9 1.0
NH1 A:ARG334 4.9 38.9 1.0
NH1 A:ARG331 4.9 38.9 1.0
N A:GLY50 5.0 39.8 1.0
CZ A:ARG334 5.0 41.6 1.0

Fluorine binding site 3 out of 18 in 7pli

Go back to Fluorine Binding Sites List in 7pli
Fluorine binding site 3 out of 18 in the Dead-Box Helicase Dbpa Bound to Single Stranded 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 Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:41.2
occ:1.00
 F3 A:BEF501 0.0 41.2 1.0
BE A:BEF501 1.5 41.2 1.0
O2B A:ADP500 2.4 42.6 1.0
F2 A:BEF501 2.5 37.1 1.0
F1 A:BEF501 2.5 40.6 1.0
NZ A:LYS53 3.0 39.5 1.0
CA A:THR49 3.2 42.6 1.0
PB A:ADP500 3.4 38.6 1.0
CG2 A:THR49 3.5 42.2 1.0
CB A:THR49 3.5 42.0 1.0
CE A:LYS53 3.6 42.6 1.0
N A:GLY50 3.7 39.8 1.0
O3B A:ADP500 3.7 41.8 1.0
O1B A:ADP500 3.9 36.5 1.0
C A:THR49 4.0 42.4 1.0
O A:HOH604 4.1 37.7 1.0
N A:THR49 4.2 42.9 1.0
MG A:MG502 4.2 40.0 1.0
CB A:ALA185 4.4 44.6 1.0
O A:LYS48 4.4 47.4 1.0
OE2 A:GLU154 4.4 45.7 1.0
NH2 A:ARG331 4.5 40.6 1.0
C A:LYS48 4.6 45.6 1.0
NH1 A:ARG334 4.7 38.9 1.0
O3A A:ADP500 4.7 40.2 1.0
NH2 A:ARG334 4.9 40.9 1.0
CA A:GLY50 4.9 41.5 1.0
OG1 A:THR49 5.0 43.7 1.0

Fluorine binding site 4 out of 18 in 7pli

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Fluorine binding site 4 out of 18 in the Dead-Box Helicase Dbpa Bound to Single Stranded 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 Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:35.1
occ:1.00
 F1 B:BEF501 0.0 35.1 1.0
BE B:BEF501 1.5 35.8 1.0
O1B B:ADP500 2.3 34.6 1.0
F3 B:BEF501 2.5 36.2 1.0
F2 B:BEF501 2.6 31.6 1.0
NH1 B:ARG334 2.7 35.4 1.0
NH1 B:ARG331 3.1 36.8 1.0
NH2 B:ARG334 3.1 33.3 1.0
NH2 B:ARG331 3.1 35.5 1.0
CZ B:ARG334 3.3 34.6 1.0
N B:GLY50 3.3 36.1 1.0
CZ B:ARG331 3.5 37.3 1.0
CB B:THR49 3.6 34.1 1.0
CA B:THR49 3.8 35.7 1.0
PB B:ADP500 3.8 28.0 1.0
CG2 B:THR49 3.9 32.7 1.0
C B:THR49 4.0 35.8 1.0
CA B:GLY304 4.1 35.5 1.0
N B:GLY304 4.2 39.7 1.0
CA B:GLY50 4.2 35.6 1.0
O B:HOH601 4.4 29.6 1.0
O3B B:ADP500 4.4 34.7 1.0
MG B:MG502 4.5 34.6 1.0
O3A B:ADP500 4.6 35.0 1.0
C B:GLY304 4.6 36.3 1.0
NE B:ARG334 4.6 34.4 1.0
O B:GLY330 4.7 35.3 1.0
NZ B:LYS53 4.7 35.1 1.0
O B:GLY304 4.7 36.8 1.0
OG1 B:THR49 4.8 36.9 1.0
O2B B:ADP500 4.8 36.0 1.0
NE B:ARG331 4.9 37.6 1.0
O1A B:ADP500 4.9 40.8 1.0

Fluorine binding site 5 out of 18 in 7pli

Go back to Fluorine Binding Sites List in 7pli
Fluorine binding site 5 out of 18 in the Dead-Box Helicase Dbpa Bound to Single Stranded 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 Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:31.6
occ:1.00
 F2 B:BEF501 0.0 31.6 1.0
BE B:BEF501 1.6 35.8 1.0
MG B:MG502 2.0 34.6 1.0
O1B B:ADP500 2.4 34.6 1.0
F3 B:BEF501 2.5 36.2 1.0
F1 B:BEF501 2.6 35.1 1.0
O B:HOH601 2.7 29.6 1.0
O3B B:ADP500 2.7 34.7 1.0
O B:HOH603 3.0 34.5 1.0
O B:HOH604 3.0 34.7 1.0
PB B:ADP500 3.0 28.0 1.0
CA B:GLY304 3.4 35.5 1.0
OE2 B:GLU154 3.5 37.3 1.0
O1A B:ADP500 3.9 40.8 1.0
NZ B:LYS53 4.0 35.1 1.0
N B:GLY304 4.0 39.7 1.0
O B:HOH602 4.1 36.6 1.0
NH2 B:ARG334 4.1 33.3 1.0
O B:GLY304 4.2 36.8 1.0
O2B B:ADP500 4.2 36.0 1.0
O3A B:ADP500 4.2 35.0 1.0
C B:GLY304 4.2 36.3 1.0
CD B:GLU154 4.6 39.0 1.0
PA B:ADP500 4.7 33.6 1.0
NH1 B:ARG331 4.7 36.8 1.0
NH1 B:ARG334 4.9 35.4 1.0
N B:GLY50 4.9 36.1 1.0
CZ B:ARG334 5.0 34.6 1.0

Fluorine binding site 6 out of 18 in 7pli

Go back to Fluorine Binding Sites List in 7pli
Fluorine binding site 6 out of 18 in the Dead-Box Helicase Dbpa Bound to Single Stranded 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 Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:36.2
occ:1.00
 F3 B:BEF501 0.0 36.2 1.0
BE B:BEF501 1.5 35.8 1.0
NZ B:LYS53 2.5 35.1 1.0
F2 B:BEF501 2.5 31.6 1.0
O1B B:ADP500 2.5 34.6 1.0
F1 B:BEF501 2.5 35.1 1.0
CA B:THR49 3.3 35.7 1.0
PB B:ADP500 3.4 28.0 1.0
CG2 B:THR49 3.6 32.7 1.0
CE B:LYS53 3.6 37.9 1.0
CB B:THR49 3.7 34.1 1.0
O2B B:ADP500 3.8 36.0 1.0
N B:GLY50 3.8 36.1 1.0
O B:HOH603 3.9 34.5 1.0
O3B B:ADP500 3.9 34.7 1.0
MG B:MG502 4.0 34.6 1.0
C B:THR49 4.1 35.8 1.0
N B:THR49 4.2 35.2 1.0
O B:LYS48 4.3 38.9 1.0
CB B:ALA185 4.4 35.6 1.0
OE2 B:GLU154 4.4 37.3 1.0
CD B:LYS53 4.5 40.6 1.0
C B:LYS48 4.6 38.6 1.0
NH2 B:ARG331 4.6 35.5 1.0
O3A B:ADP500 4.9 35.0 1.0

Fluorine binding site 7 out of 18 in 7pli

Go back to Fluorine Binding Sites List in 7pli
Fluorine binding site 7 out of 18 in the Dead-Box Helicase Dbpa Bound to Single Stranded 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 Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F501

b:44.9
occ:1.00
 F1 E:BEF501 0.0 44.9 1.0
BE E:BEF501 1.5 47.0 1.0
O1B E:ADP500 2.5 45.1 1.0
F3 E:BEF501 2.5 50.8 1.0
F2 E:BEF501 2.6 47.4 1.0
NH1 E:ARG334 2.8 43.5 1.0
NH1 E:ARG331 2.8 41.9 1.0
NH2 E:ARG334 2.9 43.5 1.0
NH2 E:ARG331 3.0 44.2 1.0
CZ E:ARG334 3.3 44.8 1.0
CZ E:ARG331 3.4 43.4 1.0
CA E:GLY304 3.6 43.7 1.0
N E:GLY50 3.8 44.1 1.0
N E:GLY304 3.8 44.5 1.0
PB E:ADP500 4.0 45.3 1.0
CB E:THR49 4.0 45.0 1.0
O E:HOH601 4.1 46.2 1.0
C E:GLY304 4.1 47.1 1.0
O E:GLY304 4.2 44.8 1.0
CA E:THR49 4.3 47.0 1.0
CG2 E:THR49 4.3 41.6 1.0
MG E:MG502 4.4 47.4 1.0
C E:THR49 4.5 46.6 1.0
NE E:ARG334 4.6 44.1 1.0
O3A E:ADP500 4.6 47.9 1.0
O3B E:ADP500 4.6 45.9 1.0
CA E:GLY50 4.6 44.7 1.0
NE E:ARG331 4.7 44.1 1.0
OE2 E:GLU154 4.7 54.5 1.0
O1A E:ADP500 4.8 49.1 1.0
O E:GLY330 4.8 43.9 1.0
O E:LEU305 4.8 43.5 1.0
N E:LEU305 4.9 45.7 1.0
O E:HOH602 5.0 51.0 1.0

Fluorine binding site 8 out of 18 in 7pli

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Fluorine binding site 8 out of 18 in the Dead-Box Helicase Dbpa Bound to Single Stranded 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 Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F501

b:47.4
occ:1.00
 F2 E:BEF501 0.0 47.4 1.0
BE E:BEF501 1.6 47.0 1.0
MG E:MG502 2.0 47.4 1.0
O1B E:ADP500 2.3 45.1 1.0
F3 E:BEF501 2.5 50.8 1.0
O E:HOH601 2.5 46.2 1.0
F1 E:BEF501 2.6 44.9 1.0
O E:HOH604 2.8 52.6 1.0
O3B E:ADP500 2.8 45.9 1.0
O E:HOH602 2.8 51.0 1.0
PB E:ADP500 3.0 45.3 1.0
OE2 E:GLU154 3.3 54.5 1.0
CA E:GLY304 3.5 43.7 1.0
O1A E:ADP500 3.9 49.1 1.0
O E:HOH603 4.0 45.8 1.0
N E:GLY304 4.1 44.5 1.0
O3A E:ADP500 4.1 47.9 1.0
NH2 E:ARG334 4.1 43.5 1.0
O2B E:ADP500 4.1 46.6 1.0
NZ E:LYS53 4.2 46.8 1.0
O E:GLY304 4.2 44.8 1.0
C E:GLY304 4.3 47.1 1.0
CD E:GLU154 4.5 54.7 1.0
PA E:ADP500 4.7 44.3 1.0
NH1 E:ARG331 4.9 41.9 1.0

Fluorine binding site 9 out of 18 in 7pli

Go back to Fluorine Binding Sites List in 7pli
Fluorine binding site 9 out of 18 in the Dead-Box Helicase Dbpa Bound to Single Stranded 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 Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F501

b:50.8
occ:1.00
 F3 E:BEF501 0.0 50.8 1.0
BE E:BEF501 1.5 47.0 1.0
O1B E:ADP500 2.4 45.1 1.0
F2 E:BEF501 2.5 47.4 1.0
F1 E:BEF501 2.5 44.9 1.0
NZ E:LYS53 2.8 46.8 1.0
CA E:THR49 3.4 47.0 1.0
PB E:ADP500 3.5 45.3 1.0
CG2 E:THR49 3.6 41.6 1.0
CB E:THR49 3.7 45.0 1.0
O E:HOH604 3.7 52.6 1.0
N E:GLY50 3.9 44.1 1.0
O2B E:ADP500 3.9 46.6 1.0
CE E:LYS53 4.0 49.3 1.0
OE2 E:GLU154 4.2 54.5 1.0
MG E:MG502 4.2 47.4 1.0
C E:THR49 4.2 46.6 1.0
O3B E:ADP500 4.2 45.9 1.0
N E:THR49 4.3 48.6 1.0
NH2 E:ARG331 4.3 44.2 1.0
CB E:ALA185 4.3 47.8 1.0
O E:LYS48 4.4 48.8 1.0
C E:LYS48 4.7 49.3 1.0
CD E:LYS53 4.8 49.1 1.0
O3A E:ADP500 4.8 47.9 1.0
NH1 E:ARG334 4.8 43.5 1.0
NH2 E:ARG334 4.8 43.5 1.0
O E:HOH602 4.9 51.0 1.0
O E:HOH601 4.9 46.2 1.0
ND1 E:HIS327 5.0 49.8 1.0

Fluorine binding site 10 out of 18 in 7pli

Go back to Fluorine Binding Sites List in 7pli
Fluorine binding site 10 out of 18 in the Dead-Box Helicase Dbpa Bound to Single Stranded 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 Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F501

b:51.0
occ:1.00
 F1 J:BEF501 0.0 51.0 1.0
BE J:BEF501 1.5 49.8 1.0
O2B J:ADP500 2.2 49.0 1.0
NH1 J:ARG334 2.5 48.4 1.0
F3 J:BEF501 2.5 48.8 1.0
F2 J:BEF501 2.6 47.3 1.0
NH2 J:ARG334 2.9 47.8 1.0
CZ J:ARG334 3.1 48.3 1.0
NH1 J:ARG331 3.1 45.9 1.0
N J:GLY50 3.2 46.0 1.0
NH2 J:ARG331 3.4 45.8 1.0
PB J:ADP500 3.7 46.8 1.0
CZ J:ARG331 3.7 47.1 1.0
CB J:THR49 3.8 46.6 1.0
CA J:THR49 3.9 50.9 1.0
C J:THR49 4.0 50.4 1.0
CA J:GLY50 4.0 47.0 1.0
CA J:GLY304 4.2 48.9 1.0
CG2 J:THR49 4.2 49.7 1.0
O3B J:ADP500 4.3 53.4 1.0
O J:HOH601 4.3 51.2 1.0
O3A J:ADP500 4.3 49.6 1.0
NE J:ARG334 4.4 47.0 1.0
N J:GLY304 4.4 51.1 1.0
MG J:MG502 4.5 51.3 1.0
O J:GLY304 4.5 47.9 1.0
C J:GLY304 4.6 48.5 1.0
O2A J:ADP500 4.6 54.3 1.0
NZ J:LYS53 4.7 53.0 1.0
O J:GLY330 4.7 49.6 1.0
O1B J:ADP500 4.7 52.7 1.0
O J:HOH604 4.9 56.5 1.0
OG1 J:THR49 5.0 48.8 1.0
NE J:ARG331 5.0 49.0 1.0

Reference:

J.P.Wurm, J.P.Wurm. N/A N/A.
Page generated: Fri Aug 2 11:08:17 2024

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