Fluorine in PDB 3i61: Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride

The structure of Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride, PDB code: 3i61 was solved by M.Del Campo, A.M.Lambowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.37 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.294, 126.082, 55.721, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.1

The structure of Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride (pdb code 3i61). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride, PDB code: 3i61:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:F900 b:15.7 occ:1.00 F1 A:BEF900 0.0 15.7 1.0 BE A:BEF900 1.7 13.7 1.0 NZ A:LYS158 2.6 11.0 1.0 O A:HOH1026 2.8 11.5 1.0 O1B A:ADP1000 2.8 14.2 1.0 F2 A:BEF900 2.9 14.7 1.0 F3 A:BEF900 3.0 15.4 1.0 CE A:LYS158 3.1 12.2 1.0 CA A:THR154 3.4 12.8 1.0 O A:HOH1011 3.4 9.8 1.0 CG2 A:THR154 3.7 12.3 1.0 PB A:ADP1000 3.7 14.9 1.0 O A:HOH1001 3.8 10.6 1.0 CB A:THR154 3.9 12.7 1.0 O3B A:ADP1000 4.0 15.6 1.0 CB A:ALA306 4.0 16.3 1.0 N A:THR154 4.0 13.0 1.0 O2B A:ADP1000 4.1 14.0 1.0 N A:GLY155 4.1 13.3 1.0 MG A:MG800 4.3 18.1 1.0 O A:LYS153 4.3 13.0 1.0 C A:THR154 4.3 13.0 1.0 OE2 A:GLU268 4.3 16.1 1.0 C A:LYS153 4.4 13.5 1.0 N A:ALA306 4.5 15.9 1.0 O A:ALA152 4.6 13.8 1.0 CD A:LYS158 4.6 12.7 1.0 NH2 A:ARG466 4.7 12.7 1.0 CA A:ALA306 4.8 16.3 1.0 ND1 A:HIS462 4.8 10.9 1.0 CE1 A:HIS462 4.9 12.2 1.0

Fluorine binding site 2 out of 3 in the Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:F900 b:14.7 occ:1.00 F2 A:BEF900 0.0 14.7 1.0 BE A:BEF900 1.7 13.7 1.0 MG A:MG800 1.8 18.1 1.0 O A:HOH1004 2.6 11.0 1.0 O A:HOH1001 2.6 10.6 1.0 O A:HOH1002 2.7 10.2 1.0 O2B A:ADP1000 2.8 14.0 1.0 O1B A:ADP1000 2.9 14.2 1.0 F1 A:BEF900 2.9 15.7 1.0 F3 A:BEF900 3.0 15.4 1.0 OE2 A:GLU268 3.1 16.1 1.0 CA A:GLY439 3.2 15.4 1.0 PB A:ADP1000 3.3 14.9 1.0 O A:HOH1011 3.5 9.8 1.0 O A:HOH1003 3.8 12.8 1.0 N A:GLY439 3.9 15.5 1.0 O A:GLY439 3.9 14.9 1.0 O A:HOH1026 4.0 11.5 1.0 C A:GLY439 4.0 15.1 1.0 NH2 A:ARG469 4.3 11.6 1.0 CD A:GLU268 4.4 17.1 1.0 CE A:LYS158 4.4 12.2 1.0 O3B A:ADP1000 4.5 15.6 1.0 O3A A:ADP1000 4.5 15.0 1.0 NZ A:LYS158 4.5 11.0 1.0 O2A A:ADP1000 4.7 14.3 1.0 NH1 A:ARG466 4.7 12.6 1.0 OD2 A:ASP267 5.0 19.7 1.0

Fluorine binding site 3 out of 3 in the Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of MSS116P Bound to Ssrna and Adp-Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:F900 b:15.4 occ:1.00 F3 A:BEF900 0.0 15.4 1.0 BE A:BEF900 1.8 13.7 1.0 NH1 A:ARG469 2.6 9.5 1.0 NH1 A:ARG466 2.7 12.6 1.0 NH2 A:ARG466 2.7 12.7 1.0 O1B A:ADP1000 2.8 14.2 1.0 F2 A:BEF900 3.0 14.7 1.0 F1 A:BEF900 3.0 15.7 1.0 CZ A:ARG466 3.1 13.0 1.0 NH2 A:ARG469 3.1 11.6 1.0 O A:HOH1011 3.2 9.8 1.0 CZ A:ARG469 3.3 10.6 1.0 CB A:THR154 3.7 12.7 1.0 N A:GLY155 3.8 13.3 1.0 CG2 A:THR154 3.9 12.3 1.0 CA A:THR154 4.0 12.8 1.0 CA A:GLY439 4.1 15.4 1.0 N A:GLY439 4.1 15.5 1.0 PB A:ADP1000 4.2 14.9 1.0 O A:GLY439 4.3 14.9 1.0 C A:THR154 4.3 13.0 1.0 C A:GLY439 4.4 15.1 1.0 O A:GLY465 4.4 11.8 1.0 NE A:ARG466 4.4 12.6 1.0 NE A:ARG469 4.6 11.8 1.0 O A:HOH1002 4.6 10.2 1.0 MG A:MG800 4.7 18.1 1.0 O2B A:ADP1000 4.7 14.0 1.0 CA A:GLY155 4.7 13.4 1.0 O3A A:ADP1000 4.9 15.0 1.0

M.Del Campo, A.M.Lambowitz. Structure of the Yeast Dead Box Protein MSS116P Reveals Two Wedges That Crimp Rna Mol.Cell V. 35 598 2009.
ISSN: ISSN 1097-2765
PubMed: 19748356
DOI: 10.1016/J.MOLCEL.2009.07.032