Atomistry » Fluorine » PDB 5j8m-5jw1 » 5js2
Atomistry »
  Fluorine »
    PDB 5j8m-5jw1 »
      5js2 »

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: Sun Dec 13 12:25:41 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy