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

Protein crystallography data

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

Other elements in 5js2:

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

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

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 5js2

Go back to Fluorine Binding Sites List in 5js2
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 5js2

Go back to Fluorine Binding Sites List in 5js2
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 5js2

Go back to Fluorine Binding Sites List in 5js2
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

Reference:

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
Page generated: Tue Jul 15 04:32:29 2025

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