Fluorine in PDB 5js2: Human Argonaute-2 Bound to A Modified Sirna

The structure of Human Argonaute-2 Bound to A Modified Sirna, PDB code: 5js2 was solved by N.T.Schirle, I.J.Macrae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.98 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.102, 107.552, 68.893, 90.00, 107.39, 90.00
R / Rfree (%)	22.2 / 26.1

The structure of Human Argonaute-2 Bound to A Modified Sirna also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Human Argonaute-2 Bound to A Modified Sirna (pdb code 5js2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Argonaute-2 Bound to A Modified Sirna, PDB code: 5js2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Human Argonaute-2 Bound to A Modified Sirna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Argonaute-2 Bound to A Modified Sirna within 5.0Å range: probe atom residue distance (Å) B Occ B:F902 b:62.9 occ:1.00 F2' B:F2T902 0.0 62.9 1.0 C2' B:F2T902 1.4 68.3 1.0 C1' B:F2T902 2.1 69.7 1.0 C3' B:F2T902 2.2 71.3 1.0 O3' B:F2T902 2.4 69.3 1.0 C4' B:F2T902 2.7 70.0 1.0 O4' B:F2T902 2.9 71.2 1.0 O5' B:6NW903 3.0 57.0 1.0 P B:6NW903 3.3 64.2 1.0 N1 B:F2T902 3.4 69.0 1.0 O2 B:F2T902 3.7 69.2 1.0 CD A:LYS566 3.8 61.8 1.0 O A:ASN562 3.9 64.5 1.0 O4' B:6NW903 3.9 64.7 1.0 C2 B:F2T902 4.0 69.6 1.0 C A:ASN562 4.0 64.8 1.0 CA A:LEU563 4.1 66.0 1.0 N A:LEU563 4.1 65.2 1.0 CD1 A:LEU563 4.1 66.5 1.0 C5' B:F2T902 4.2 68.2 1.0 OP2 B:6NW903 4.2 60.0 1.0 C5' B:6NW903 4.2 58.1 1.0 C6 B:F2T902 4.3 67.5 1.0 NZ A:LYS566 4.3 57.0 1.0 CB A:ASN562 4.4 68.7 1.0 C4' B:6NW903 4.5 59.9 1.0 CB A:LEU563 4.6 63.0 1.0 CE A:LYS566 4.7 50.8 1.0 O A:THR559 4.7 76.1 1.0 C8 B:6NW903 4.9 65.0 1.0 CG A:LYS566 4.9 61.7 1.0 CA A:ASN562 4.9 70.6 1.0 O5' B:F2T902 5.0 63.8 1.0 CG A:LEU563 5.0 64.7 1.0

Fluorine binding site 2 out of 3 in the Human Argonaute-2 Bound to A Modified Sirna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Argonaute-2 Bound to A Modified Sirna within 5.0Å range: probe atom residue distance (Å) B Occ B:F904 b:76.0 occ:1.00 F2' B:UFT904 0.0 76.0 1.0 C2' B:UFT904 1.3 69.6 1.0 C1' B:UFT904 2.2 70.1 1.0 C3' B:UFT904 2.2 66.3 1.0 O3' B:UFT904 2.5 61.9 1.0 C4' B:UFT904 2.7 60.3 1.0 O4' B:UFT904 2.8 70.3 1.0 O5' B:6OO905 3.0 71.9 1.0 N1 B:UFT904 3.3 72.2 1.0 P B:6OO905 3.4 60.5 1.0 O2 B:UFT904 3.5 66.4 1.0 O4' B:6OO905 3.8 71.8 1.0 C2 B:UFT904 3.8 71.5 1.0 C5' B:6OO905 3.9 65.4 1.0 CD A:ARG795 4.1 54.8 1.0 SP1 B:6OO905 4.1 61.5 1.0 C5' B:UFT904 4.2 54.0 1.0 CD1 A:ILE756 4.2 62.9 1.0 C6 B:UFT904 4.3 66.8 1.0 C4' B:6OO905 4.5 74.1 1.0 NE A:ARG795 4.5 68.5 1.0 C6 B:6OO905 4.5 78.6 1.0 O5' B:UFT904 4.7 55.0 1.0 OP2 B:6OO905 4.7 48.9 1.0 NH1 A:ARG795 4.8 65.2 1.0 C1' B:6OO905 4.8 78.4 1.0 N1 B:6OO905 4.8 80.3 1.0 CZ A:ARG795 4.8 73.2 1.0

Fluorine binding site 3 out of 3 in the Human Argonaute-2 Bound to A Modified Sirna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Argonaute-2 Bound to A Modified Sirna within 5.0Å range: probe atom residue distance (Å) B Occ B:F906 b:98.2 occ:0.95 F2' B:UFT906 0.0 98.2 0.9 C2' B:UFT906 1.4 97.7 0.9 C3' B:UFT906 2.3 95.8 0.9 C1' B:UFT906 2.5 0.9 1.0 O3' B:UFT906 2.7 93.1 0.9 C4' B:UFT906 3.1 96.9 0.9 O4' B:UFT906 3.3 96.7 0.9 N1 B:UFT906 3.4 0.9 1.0 C6 B:UFT906 3.8 98.0 0.9 C5' B:UFT906 4.4 86.0 0.9 C2 B:UFT906 4.5 0.1 1.0 O2 B:UFT906 4.8 99.7 0.9 O5' B:UFT906 4.9 83.5 0.9

N.T.Schirle, G.A.Kinberger, H.F.Murray, W.F.Lima, T.P.Prakash, I.J.Macrae. Structural Analysis of Human Argonaute-2 Bound to A Modified Sirna Guide. J.Am.Chem.Soc. V. 138 8694 2016.
ISSN: ESSN 1520-5126
PubMed: 27380263
DOI: 10.1021/JACS.6B04454