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Fluorine in PDB 3pew: S. Cerevisiae DBP5 L327V Bound to Rna and Adp BEF3

Enzymatic activity of S. Cerevisiae DBP5 L327V Bound to Rna and Adp BEF3

All present enzymatic activity of S. Cerevisiae DBP5 L327V Bound to Rna and Adp BEF3:
3.6.4.13;

Protein crystallography data

The structure of S. Cerevisiae DBP5 L327V Bound to Rna and Adp BEF3, PDB code: 3pew was solved by B.Montpetit, N.D.Thomsen, K.J.Helmke, M.A.Seeliger, J.M.Berger, K.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.36 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.309, 90.810, 105.123, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.9

Other elements in 3pew:

The structure of S. Cerevisiae DBP5 L327V Bound to Rna and Adp BEF3 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the S. Cerevisiae DBP5 L327V Bound to Rna and Adp BEF3 (pdb code 3pew). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the S. Cerevisiae DBP5 L327V Bound to Rna and Adp BEF3, PDB code: 3pew:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3pew

Go back to Fluorine Binding Sites List in 3pew
Fluorine binding site 1 out of 3 in the S. Cerevisiae DBP5 L327V Bound to 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 S. Cerevisiae DBP5 L327V Bound to Rna and Adp BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:8.9
occ:1.00
F1 A:BEF1002 0.0 8.9 1.0
BE A:BEF1002 1.5 9.5 1.0
F3 A:BEF1002 2.5 8.7 1.0
F2 A:BEF1002 2.5 9.0 1.0
O1B A:ADP1000 2.5 8.5 1.0
NH1 A:ARG429 2.8 8.7 1.0
NH1 A:ARG426 2.9 8.7 1.0
NH2 A:ARG426 3.0 9.4 1.0
O A:HOH1062 3.2 15.3 1.0
NH2 A:ARG429 3.2 8.2 1.0
O A:HOH1014 3.3 11.0 1.0
CZ A:ARG426 3.4 7.0 1.0
CZ A:ARG429 3.4 8.4 1.0
N A:GLY141 3.7 6.9 1.0
CB A:SER140 3.8 8.8 1.0
CA A:SER140 3.9 8.6 1.0
PB A:ADP1000 4.0 8.6 1.0
CA A:GLY393 4.1 8.4 1.0
N A:GLY393 4.2 8.9 1.0
MG A:MG1001 4.3 8.8 1.0
C A:SER140 4.4 6.3 1.0
O A:HOH1107 4.4 7.8 1.0
O2B A:ADP1000 4.5 8.7 1.0
O A:GLY425 4.6 8.9 1.0
C A:GLY393 4.6 8.6 1.0
O A:GLY393 4.6 8.5 1.0
CA A:GLY141 4.7 8.1 1.0
NE A:ARG429 4.7 9.5 1.0
O A:HOH1011 4.7 8.9 1.0
NE A:ARG426 4.7 8.5 1.0
O3A A:ADP1000 4.7 8.6 1.0
OE2 A:GLU240 4.9 9.9 1.0
O3B A:ADP1000 5.0 8.5 1.0

Fluorine binding site 2 out of 3 in 3pew

Go back to Fluorine Binding Sites List in 3pew
Fluorine binding site 2 out of 3 in the S. Cerevisiae DBP5 L327V Bound to 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 S. Cerevisiae DBP5 L327V Bound to Rna and Adp BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:9.0
occ:1.00
F2 A:BEF1002 0.0 9.0 1.0
BE A:BEF1002 1.5 9.5 1.0
F3 A:BEF1002 2.4 8.7 1.0
F1 A:BEF1002 2.5 8.9 1.0
O1B A:ADP1000 2.6 8.5 1.0
O A:HOH1062 2.8 15.3 1.0
O A:HOH1011 2.9 8.9 1.0
NZ A:LYS144 2.9 8.0 1.0
CE A:LYS144 3.3 8.5 1.0
CA A:SER140 3.5 8.6 1.0
O A:HOH1014 3.5 11.0 1.0
PB A:ADP1000 3.6 8.6 1.0
O A:HOH1017 3.9 8.4 1.0
CB A:ALA272 3.9 9.2 1.0
N A:GLY141 4.0 6.9 1.0
O2B A:ADP1000 4.0 8.7 1.0
O3B A:ADP1000 4.0 8.5 1.0
CB A:SER140 4.1 8.8 1.0
MG A:MG1001 4.1 8.8 1.0
N A:SER140 4.2 9.7 1.0
O A:GLN139 4.3 8.1 1.0
C A:SER140 4.3 6.3 1.0
N A:ALA272 4.5 6.9 1.0
C A:GLN139 4.5 8.8 1.0
OE2 A:GLU240 4.6 9.9 1.0
NH1 A:ARG426 4.6 8.7 1.0
CA A:ALA272 4.7 8.1 1.0
O A:SER138 4.8 9.1 1.0
CD A:LYS144 4.9 9.1 1.0
NH1 A:ARG429 4.9 8.7 1.0
ND1 A:HIS422 5.0 11.3 1.0
O A:HOH1231 5.0 19.1 1.0

Fluorine binding site 3 out of 3 in 3pew

Go back to Fluorine Binding Sites List in 3pew
Fluorine binding site 3 out of 3 in the S. Cerevisiae DBP5 L327V Bound to 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 S. Cerevisiae DBP5 L327V Bound to Rna and Adp BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:8.7
occ:1.00
F3 A:BEF1002 0.0 8.7 1.0
BE A:BEF1002 1.5 9.5 1.0
MG A:MG1001 2.0 8.8 1.0
F2 A:BEF1002 2.4 9.0 1.0
F1 A:BEF1002 2.5 8.9 1.0
O1B A:ADP1000 2.6 8.5 1.0
O A:HOH1017 2.9 8.4 1.0
O2B A:ADP1000 2.9 8.7 1.0
O A:HOH1096 2.9 8.1 1.0
O A:HOH1107 3.0 7.8 1.0
PB A:ADP1000 3.3 8.6 1.0
OE2 A:GLU240 3.3 9.9 1.0
O A:HOH1014 3.4 11.0 1.0
O A:HOH1011 3.5 8.9 1.0
CA A:GLY393 3.5 8.4 1.0
N A:GLY393 4.1 8.9 1.0
O A:HOH1010 4.1 7.9 1.0
NH2 A:ARG429 4.1 8.2 1.0
O A:GLY393 4.3 8.5 1.0
O A:HOH1062 4.3 15.3 1.0
CE A:LYS144 4.4 8.5 1.0
C A:GLY393 4.4 8.6 1.0
O3B A:ADP1000 4.4 8.5 1.0
O3A A:ADP1000 4.4 8.6 1.0
NZ A:LYS144 4.5 8.0 1.0
CD A:GLU240 4.5 9.0 1.0
NH2 A:ARG426 4.5 9.4 1.0
NH1 A:ARG426 4.8 8.7 1.0
NH1 A:ARG429 4.9 8.7 1.0
O2A A:ADP1000 4.9 8.8 1.0
OE1 A:GLU240 4.9 10.7 1.0
CZ A:ARG429 5.0 8.4 1.0

Reference:

B.Montpetit, N.D.Thomsen, K.J.Helmke, M.A.Seeliger, J.M.Berger, K.Weis. A Conserved Mechanism of Dead-Box Atpase Activation By Nucleoporins and Insp(6) in Mrna Export. Nature V. 472 238 2011.
ISSN: ISSN 0028-0836
PubMed: 21441902
DOI: 10.1038/NATURE09862
Page generated: Sun Dec 13 11:53:07 2020

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