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

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

The structure of S. Cerevisiae DBP5 Bound to Rna and Adp BEF3, PDB code: 3pey 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)	45.47 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.136, 92.206, 104.524, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 18

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

Magnesium

(Mg)

4 atoms

The binding sites of Fluorine atom in the S. Cerevisiae DBP5 Bound to Rna and Adp BEF3 (pdb code 3pey). 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 Bound to Rna and Adp BEF3, PDB code: 3pey:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the S. Cerevisiae DBP5 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 Bound to Rna and Adp BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:7.1 occ:1.00 F1 A:BEF1002 0.0 7.1 1.0 BE A:BEF1002 1.5 6.9 1.0 F3 A:BEF1002 2.5 7.0 1.0 F2 A:BEF1002 2.5 6.9 1.0 O1B A:ADP1000 2.5 6.9 1.0 NH1 A:ARG429 2.8 6.6 1.0 NH1 A:ARG426 2.9 7.1 1.0 NH2 A:ARG426 3.0 6.7 1.0 O A:HOH1168 3.2 15.2 1.0 NH2 A:ARG429 3.2 6.7 1.0 O A:HOH1011 3.2 7.7 1.0 CZ A:ARG426 3.4 5.3 1.0 CZ A:ARG429 3.4 6.2 1.0 N A:GLY141 3.7 6.3 1.0 CB A:SER140 3.9 9.2 1.0 CA A:SER140 3.9 6.5 1.0 PB A:ADP1000 4.0 7.0 1.0 CA A:GLY393 4.1 5.9 1.0 N A:GLY393 4.2 5.9 1.0 C A:SER140 4.3 5.7 1.0 MG A:MG1001 4.3 7.1 1.0 O A:HOH1481 4.5 6.5 1.0 O2B A:ADP1000 4.5 7.0 1.0 O A:GLY425 4.6 6.8 1.0 C A:GLY393 4.6 6.1 1.0 CA A:GLY141 4.6 6.2 1.0 O A:GLY393 4.6 6.8 1.0 O3A A:ADP1000 4.7 6.9 1.0 NE A:ARG429 4.7 7.2 1.0 NE A:ARG426 4.7 7.8 1.0 O A:HOH1012 4.7 7.1 1.0 O3B A:ADP1000 4.9 6.9 1.0 NZ A:LYS144 4.9 6.5 1.0 OE2 A:GLU240 4.9 7.8 1.0

Fluorine binding site 2 out of 3 in the S. Cerevisiae DBP5 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 Bound to Rna and Adp BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:6.9 occ:1.00 F2 A:BEF1002 0.0 6.9 1.0 BE A:BEF1002 1.5 6.9 1.0 F3 A:BEF1002 2.5 7.0 1.0 F1 A:BEF1002 2.5 7.1 1.0 O1B A:ADP1000 2.6 6.9 1.0 NZ A:LYS144 2.8 6.5 1.0 O A:HOH1012 2.9 7.1 1.0 O A:HOH1168 2.9 15.2 1.0 CE A:LYS144 3.3 6.0 1.0 O A:HOH1011 3.4 7.7 1.0 CA A:SER140 3.5 6.5 1.0 PB A:ADP1000 3.6 7.0 1.0 O A:HOH1010 3.8 7.4 1.0 CB A:ALA272 4.0 6.4 1.0 O3B A:ADP1000 4.0 6.9 1.0 N A:GLY141 4.0 6.3 1.0 O2B A:ADP1000 4.0 7.0 1.0 MG A:MG1001 4.0 7.1 1.0 CB A:SER140 4.1 9.2 1.0 N A:SER140 4.2 6.6 1.0 C A:SER140 4.3 5.7 1.0 O A:GLN139 4.3 6.4 1.0 N A:ALA272 4.5 5.4 1.0 C A:GLN139 4.5 5.6 1.0 OE2 A:GLU240 4.6 7.8 1.0 NH1 A:ARG426 4.6 7.1 1.0 CD A:LYS144 4.8 6.2 1.0 CA A:ALA272 4.8 6.4 1.0 O A:SER138 4.8 7.7 1.0 ND1 A:HIS422 4.9 7.5 1.0 NH1 A:ARG429 4.9 6.6 1.0 CE1 A:HIS422 4.9 6.8 1.0 O3A A:ADP1000 5.0 6.9 1.0

Fluorine binding site 3 out of 3 in the S. Cerevisiae DBP5 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 Bound to Rna and Adp BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:7.0 occ:1.00 F3 A:BEF1002 0.0 7.0 1.0 BE A:BEF1002 1.5 6.9 1.0 MG A:MG1001 2.0 7.1 1.0 F2 A:BEF1002 2.5 6.9 1.0 F1 A:BEF1002 2.5 7.1 1.0 O1B A:ADP1000 2.6 6.9 1.0 O A:HOH1010 2.8 7.4 1.0 O A:HOH1096 2.9 6.6 1.0 O2B A:ADP1000 2.9 7.0 1.0 O A:HOH1481 3.0 6.5 1.0 O A:HOH1011 3.2 7.7 1.0 PB A:ADP1000 3.3 7.0 1.0 OE2 A:GLU240 3.3 7.8 1.0 CA A:GLY393 3.4 5.9 1.0 O A:HOH1012 3.5 7.1 1.0 N A:GLY393 4.0 5.9 1.0 O A:HOH1095 4.1 7.2 1.0 NH2 A:ARG429 4.2 6.7 1.0 O A:GLY393 4.2 6.8 1.0 C A:GLY393 4.3 6.1 1.0 CE A:LYS144 4.4 6.0 1.0 O3B A:ADP1000 4.4 6.9 1.0 O3A A:ADP1000 4.4 6.9 1.0 NZ A:LYS144 4.4 6.5 1.0 CD A:GLU240 4.4 8.8 1.0 O A:HOH1168 4.5 15.2 1.0 NH2 A:ARG426 4.5 6.7 1.0 NH1 A:ARG426 4.8 7.1 1.0 O2A A:ADP1000 4.8 7.3 1.0 NH1 A:ARG429 4.9 6.6 1.0 OE1 A:GLU240 4.9 8.3 1.0

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