Fluorine in PDB 5elx: S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3

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

The structure of S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3, PDB code: 5elx was solved by M.K.Merchant, Y.Modis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.26 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.082, 91.751, 104.521, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.8

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

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3 (pdb code 5elx). 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 Mant-Adp BEF3, PDB code: 5elx:
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 Mant-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 Mant-Adp BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:8.5 occ:1.00 F1 A:BEF503 0.0 8.5 1.0 BE A:BEF503 1.5 10.1 1.0 O1 A:M2A501 2.4 8.7 1.0 F3 A:BEF503 2.5 7.9 1.0 F2 A:BEF503 2.5 10.6 1.0 NH1 A:ARG429 2.7 6.4 1.0 NH1 A:ARG426 2.9 9.8 1.0 NH2 A:ARG426 3.1 10.3 1.0 NH2 A:ARG429 3.1 8.5 1.0 O A:HOH686 3.2 9.6 1.0 O A:HOH695 3.2 19.0 1.0 CZ A:ARG429 3.3 10.4 1.0 CZ A:ARG426 3.4 9.6 1.0 N A:GLY141 3.7 8.7 1.0 P1 A:M2A501 3.9 8.5 1.0 CB A:SER140 3.9 7.2 1.0 CA A:SER140 3.9 10.4 1.0 CA A:GLY393 4.1 8.3 1.0 N A:GLY393 4.2 7.2 1.0 MG A:MG502 4.3 7.3 1.0 C A:SER140 4.3 8.1 1.0 O3 A:M2A501 4.4 8.7 1.0 O A:HOH697 4.4 8.4 1.0 C A:GLY393 4.6 9.4 1.0 O A:GLY393 4.6 9.8 1.0 O4 A:M2A501 4.6 9.2 1.0 CA A:GLY141 4.6 8.3 1.0 NE A:ARG429 4.6 8.8 1.0 O A:GLY425 4.6 8.2 1.0 O A:HOH789 4.7 8.6 1.0 NE A:ARG426 4.7 10.7 1.0 O2 A:M2A501 4.9 6.6 1.0 NZ A:LYS144 4.9 7.9 1.0 OE2 A:GLU240 4.9 8.9 1.0

Fluorine binding site 2 out of 3 in the S. Cerevisiae DBP5 Bound to Rna and Mant-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 Mant-Adp BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:10.6 occ:1.00 F2 A:BEF503 0.0 10.6 1.0 BE A:BEF503 1.6 10.1 1.0 F3 A:BEF503 2.4 7.9 1.0 O1 A:M2A501 2.5 8.7 1.0 F1 A:BEF503 2.5 8.5 1.0 NZ A:LYS144 2.7 7.9 1.0 O A:HOH789 2.8 8.6 1.0 O A:HOH695 3.1 19.0 1.0 CE A:LYS144 3.2 8.8 1.0 O A:HOH686 3.4 9.6 1.0 P1 A:M2A501 3.5 8.5 1.0 CA A:SER140 3.5 10.4 1.0 O A:HOH692 3.7 9.1 1.0 O2 A:M2A501 3.9 6.6 1.0 O3 A:M2A501 3.9 8.7 1.0 MG A:MG502 4.0 7.3 1.0 CB A:ALA272 4.0 9.9 1.0 N A:GLY141 4.0 8.7 1.0 CB A:SER140 4.1 7.2 1.0 O A:GLN139 4.3 10.4 1.0 N A:SER140 4.3 7.3 1.0 C A:SER140 4.3 8.1 1.0 OE2 A:GLU240 4.5 8.9 1.0 N A:ALA272 4.6 6.5 1.0 NH1 A:ARG426 4.6 9.8 1.0 C A:GLN139 4.6 8.7 1.0 CD A:LYS144 4.7 8.2 1.0 CA A:ALA272 4.8 8.1 1.0 O A:SER138 4.8 8.9 0.7 O A:SER138 4.8 8.9 0.3 CE1 A:HIS422 4.9 9.8 1.0 O4 A:M2A501 4.9 9.2 1.0 ND1 A:HIS422 4.9 9.6 1.0 NH1 A:ARG429 4.9 6.4 1.0 NH2 A:ARG429 4.9 8.5 1.0

Fluorine binding site 3 out of 3 in the S. Cerevisiae DBP5 Bound to Rna and Mant-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 Mant-Adp BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:7.9 occ:1.00 F3 A:BEF503 0.0 7.9 1.0 BE A:BEF503 1.5 10.1 1.0 MG A:MG502 2.0 7.3 1.0 F2 A:BEF503 2.4 10.6 1.0 F1 A:BEF503 2.5 8.5 1.0 O1 A:M2A501 2.5 8.7 1.0 O A:HOH692 2.8 9.1 1.0 O A:HOH626 2.9 8.0 1.0 O3 A:M2A501 2.9 8.7 1.0 O A:HOH697 3.0 8.4 1.0 O A:HOH686 3.1 9.6 1.0 P1 A:M2A501 3.3 8.5 1.0 OE2 A:GLU240 3.3 8.9 1.0 CA A:GLY393 3.4 8.3 1.0 O A:HOH789 3.4 8.6 1.0 N A:GLY393 4.0 7.2 1.0 NH2 A:ARG429 4.1 8.5 1.0 O A:HOH620 4.1 8.9 1.0 O A:GLY393 4.2 9.8 1.0 C A:GLY393 4.3 9.4 1.0 CE A:LYS144 4.3 8.8 1.0 CD A:GLU240 4.4 10.1 1.0 O2 A:M2A501 4.4 6.6 1.0 O4 A:M2A501 4.4 9.2 1.0 NZ A:LYS144 4.4 7.9 1.0 O A:HOH695 4.4 19.0 1.0 NH2 A:ARG426 4.5 10.3 1.0 NH1 A:ARG426 4.7 9.8 1.0 O6 A:M2A501 4.8 5.8 1.0 OE1 A:GLU240 4.9 8.7 1.0 NH1 A:ARG429 4.9 6.4 1.0 CZ A:ARG429 4.9 10.4 1.0

E.V.Wong, W.Cao, J.Voros, M.Merchant, Y.Modis, D.D.Hackney, B.Montpetit, E.M.De La Cruz. Pi Release Limits the Intrinsic and Rna-Stimulated Atpase Cycles of Dead-Box Protein 5 (DBP5). J.Mol.Biol. V. 428 492 2016.
ISSN: ESSN 1089-8638
PubMed: 26730886
DOI: 10.1016/J.JMB.2015.12.018