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Fluorine in PDB 7liu: DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid

Enzymatic activity of DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid

All present enzymatic activity of DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid:
3.6.4.13;

Protein crystallography data

The structure of DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid, PDB code: 7liu was solved by E.J.Enemark, S.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.54 / 3.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.476, 114.476, 281.793, 90, 90, 120
R / Rfree (%) 21 / 24.1

Other elements in 7liu:

The structure of DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid (pdb code 7liu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid, PDB code: 7liu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7liu

Go back to Fluorine Binding Sites List in 7liu
Fluorine binding site 1 out of 6 in the DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:67.0
occ:1.00
 F1 A:08T902 0.0 67.0 1.0
BE A:08T902 1.5 69.3 1.0
MG A:MG901 2.0 70.7 1.0
F3 A:08T902 2.5 80.2 1.0
O3B A:08T902 2.5 65.6 1.0
F2 A:08T902 2.5 72.7 1.0
O A:HOH1003 2.7 64.5 1.0
O2B A:08T902 2.7 73.0 1.0
O A:HOH1004 2.9 58.6 1.0
O A:HOH1002 2.9 58.0 1.0
PB A:08T902 3.1 68.2 1.0
CA A:GLY504 3.4 58.2 1.0
OE2 A:GLU348 3.4 74.8 1.0
O A:GLY504 3.7 62.1 1.0
O3A A:08T902 3.8 66.3 1.0
C A:GLY504 3.9 58.9 1.0
O A:HOH1001 3.9 59.2 1.0
N A:GLY504 4.0 56.7 1.0
NH2 A:ARG534 4.0 70.6 1.0
NH1 A:ARG531 4.3 63.2 1.0
O1B A:08T902 4.5 69.4 1.0
NZ A:LYS230 4.5 76.3 1.0
NH2 A:ARG531 4.5 68.0 1.0
NH1 A:ARG534 4.5 71.7 1.0
O1A A:08T902 4.6 67.6 1.0
CD A:GLU348 4.6 70.2 1.0
CE A:LYS230 4.6 71.4 1.0
PA A:08T902 4.7 69.0 1.0
CZ A:ARG534 4.8 71.0 1.0
CZ A:ARG531 4.9 66.8 1.0

Fluorine binding site 2 out of 6 in 7liu

Go back to Fluorine Binding Sites List in 7liu
Fluorine binding site 2 out of 6 in the DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:72.7
occ:1.00
 F2 A:08T902 0.0 72.7 1.0
BE A:08T902 1.5 69.3 1.0
O3B A:08T902 2.5 65.6 1.0
F3 A:08T902 2.5 80.2 1.0
F1 A:08T902 2.5 67.0 1.0
NH2 A:ARG531 2.7 68.0 1.0
NH1 A:ARG534 2.7 71.7 1.0
NH1 A:ARG531 3.2 63.2 1.0
CZ A:ARG531 3.4 66.8 1.0
N A:GLY227 3.4 71.9 1.0
NH2 A:ARG534 3.5 70.6 1.0
CZ A:ARG534 3.5 71.0 1.0
CB A:THR226 3.5 66.2 1.0
CA A:THR226 3.7 69.0 1.0
CG2 A:THR226 3.7 69.0 1.0
PB A:08T902 3.9 68.2 1.0
C A:THR226 4.0 71.1 1.0
O3A A:08T902 4.3 66.3 1.0
CA A:GLY227 4.4 69.8 1.0
MG A:MG901 4.4 70.7 1.0
O2B A:08T902 4.4 73.0 1.0
N A:GLY504 4.5 56.7 1.0
NZ A:LYS230 4.5 76.3 1.0
CA A:GLY504 4.6 58.2 1.0
NE A:ARG531 4.7 60.3 1.0
O A:HOH1003 4.8 64.5 1.0
NE A:ARG534 4.8 69.5 1.0
O A:GLY530 4.9 67.8 1.0
OG1 A:THR226 4.9 69.3 1.0
C A:GLY504 4.9 58.9 1.0
O1B A:08T902 4.9 69.4 1.0
O A:HOH1004 5.0 58.6 1.0
O A:GLY504 5.0 62.1 1.0

Fluorine binding site 3 out of 6 in 7liu

Go back to Fluorine Binding Sites List in 7liu
Fluorine binding site 3 out of 6 in the DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:80.2
occ:1.00
 F3 A:08T902 0.0 80.2 1.0
BE A:08T902 1.5 69.3 1.0
O3B A:08T902 2.5 65.6 1.0
F1 A:08T902 2.5 67.0 1.0
F2 A:08T902 2.5 72.7 1.0
NZ A:LYS230 2.9 76.3 1.0
O A:HOH1004 3.2 58.6 1.0
CE A:LYS230 3.3 71.4 1.0
OE2 A:GLU348 3.5 74.8 1.0
MG A:MG901 3.8 70.7 1.0
PB A:08T902 3.8 68.2 1.0
O2B A:08T902 3.9 73.0 1.0
CB A:ALA383 4.0 65.3 1.0
CG2 A:THR226 4.0 69.0 1.0
CA A:THR226 4.1 69.0 1.0
NH2 A:ARG531 4.3 68.0 1.0
CE1 A:HIS527 4.4 67.7 1.0
CD A:GLU348 4.4 70.2 1.0
OE1 A:GLU348 4.4 73.3 1.0
CB A:THR226 4.4 66.2 1.0
O1B A:08T902 4.5 69.4 1.0
N A:ALA383 4.5 77.6 1.0
ND1 A:HIS527 4.5 67.4 1.0
O A:HOH1002 4.5 58.0 1.0
N A:GLY227 4.6 71.9 1.0
CD A:LYS230 4.8 64.9 1.0
CA A:ALA383 4.9 71.4 1.0
C A:THR226 4.9 71.1 1.0
N A:THR226 5.0 73.0 1.0
O3A A:08T902 5.0 66.3 1.0

Fluorine binding site 4 out of 6 in 7liu

Go back to Fluorine Binding Sites List in 7liu
Fluorine binding site 4 out of 6 in the DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F902

b:64.5
occ:1.00
 F1 B:08T902 0.0 64.5 1.0
BE B:08T902 1.5 70.1 1.0
MG B:MG901 1.9 71.3 1.0
F2 B:08T902 2.5 80.0 1.0
F3 B:08T902 2.5 73.6 1.0
O3B B:08T902 2.5 66.5 1.0
O1B B:08T902 2.7 71.2 1.0
O B:HOH1003 2.7 57.9 1.0
O B:HOH1004 2.8 60.3 1.0
O B:HOH1001 2.8 63.1 1.0
PB B:08T902 3.2 65.8 1.0
OE2 B:GLU348 3.3 67.2 1.0
CA B:GLY504 3.5 59.1 1.0
O B:HOH1002 3.9 60.1 1.0
N B:GLY504 4.0 57.5 1.0
NH2 B:ARG534 4.0 61.6 1.0
O B:GLY504 4.0 67.8 1.0
O3A B:08T902 4.1 66.0 1.0
C B:GLY504 4.2 60.8 1.0
NH1 B:ARG531 4.2 59.7 1.0
NZ B:LYS230 4.3 75.8 1.0
NH2 B:ARG531 4.4 68.7 1.0
O2B B:08T902 4.4 71.2 1.0
CD B:GLU348 4.5 66.9 1.0
CE B:LYS230 4.5 72.4 1.0
CZ B:ARG531 4.8 61.6 1.0
O2A B:08T902 4.9 72.5 1.0
PA B:08T902 5.0 69.8 1.0

Fluorine binding site 5 out of 6 in 7liu

Go back to Fluorine Binding Sites List in 7liu
Fluorine binding site 5 out of 6 in the DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F902

b:80.0
occ:1.00
 F2 B:08T902 0.0 80.0 1.0
BE B:08T902 1.5 70.1 1.0
O3B B:08T902 2.5 66.5 1.0
F1 B:08T902 2.5 64.5 1.0
F3 B:08T902 2.6 73.6 1.0
NH2 B:ARG531 2.6 68.7 1.0
NH1 B:ARG531 3.1 59.7 1.0
NH2 B:ARG534 3.1 61.6 1.0
NH1 B:ARG534 3.2 76.0 1.0
CZ B:ARG531 3.2 61.6 1.0
N B:GLY227 3.5 69.5 1.0
CB B:THR226 3.5 70.2 1.0
CA B:THR226 3.6 66.6 1.0
CZ B:ARG534 3.6 72.1 1.0
CG2 B:THR226 3.7 67.9 1.0
PB B:08T902 3.9 65.8 1.0
C B:THR226 4.0 68.5 1.0
O1B B:08T902 4.4 71.2 1.0
N B:GLY504 4.4 57.5 1.0
MG B:MG901 4.4 71.3 1.0
O3A B:08T902 4.5 66.0 1.0
CA B:GLY504 4.5 59.1 1.0
CA B:GLY227 4.5 71.5 1.0
NE B:ARG531 4.5 58.7 1.0
O B:HOH1003 4.6 57.9 1.0
NZ B:LYS230 4.6 75.8 1.0
OG1 B:THR226 4.8 77.8 1.0
O B:GLY530 4.8 66.8 1.0
C B:GLY504 4.9 60.8 1.0
N B:THR226 4.9 75.3 1.0
O B:HOH1004 4.9 60.3 1.0
O B:GLY504 4.9 67.8 1.0
NE B:ARG534 5.0 70.3 1.0
O2B B:08T902 5.0 71.2 1.0

Fluorine binding site 6 out of 6 in 7liu

Go back to Fluorine Binding Sites List in 7liu
Fluorine binding site 6 out of 6 in the DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F902

b:73.6
occ:1.00
 F3 B:08T902 0.0 73.6 1.0
BE B:08T902 1.5 70.1 1.0
O3B B:08T902 2.5 66.5 1.0
F1 B:08T902 2.5 64.5 1.0
F2 B:08T902 2.6 80.0 1.0
NZ B:LYS230 2.6 75.8 1.0
CE B:LYS230 3.2 72.4 1.0
O B:HOH1004 3.4 60.3 1.0
PB B:08T902 3.7 65.8 1.0
CA B:THR226 3.7 66.6 1.0
CB B:ALA383 3.8 71.4 1.0
OE2 B:GLU348 3.9 67.2 1.0
MG B:MG901 3.9 71.3 1.0
CG2 B:THR226 3.9 67.9 1.0
O1B B:08T902 4.0 71.2 1.0
CB B:THR226 4.2 70.2 1.0
CE1 B:HIS527 4.3 71.6 1.0
O2B B:08T902 4.3 71.2 1.0
NH2 B:ARG531 4.3 68.7 1.0
N B:GLY227 4.4 69.5 1.0
O B:GLN225 4.4 78.6 1.0
N B:ALA383 4.5 85.5 1.0
N B:THR226 4.5 75.3 1.0
ND1 B:HIS527 4.6 66.9 1.0
C B:THR226 4.6 68.5 1.0
CD B:LYS230 4.7 67.9 1.0
O B:HOH1001 4.7 63.1 1.0
CA B:ALA383 4.7 76.4 1.0
C B:GLN225 4.8 83.3 1.0
CD B:GLU348 4.8 66.9 1.0
OE1 B:GLU348 4.9 67.1 1.0
O B:ALA224 4.9 83.5 1.0

Reference:

E.J.Enemark, S.Yu. DDX3X Bound to Atp Analog and Remodeled Rna:Dna Hybrid To Be Published.
Page generated: Tue Jul 15 21:16:53 2025

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