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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:

Magnesium (Mg) 2 atoms

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

Go back to 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

Go back to 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

Go back to 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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