Fluorine in PDB 7l0z: Spinach Variant Bound to Dfhbi-1T

Protein crystallography data

The structure of Spinach Variant Bound to Dfhbi-1T, PDB code: 7l0z was solved by L.Truong, R.J.Trachman, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.26 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.564, 48.692, 30.612, 90, 91.36, 90
R / Rfree (%) 19.6 / 23.2

Other elements in 7l0z:

The structure of Spinach Variant Bound to Dfhbi-1T also contains other interesting chemical elements:

Potassium (K) 2 atoms
Sodium (Na) 2 atoms
Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Spinach Variant Bound to Dfhbi-1T (pdb code 7l0z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Spinach Variant Bound to Dfhbi-1T, PDB code: 7l0z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 7l0z

Go back to Fluorine Binding Sites List in 7l0z
Fluorine binding site 1 out of 5 in the Spinach Variant Bound to Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Spinach Variant Bound to Dfhbi-1T within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F101

b:38.6
occ:1.00
F8 G:2ZY101 0.0 38.6 1.0
C6 G:2ZY101 1.3 38.4 1.0
C1 G:2ZY101 2.3 38.0 1.0
C5 G:2ZY101 2.4 38.4 1.0
O G:HOH225 2.8 69.4 1.0
O9 G:2ZY101 2.8 38.7 1.0
O G:HOH231 3.3 58.0 1.0
O G:HOH227 3.3 39.5 1.0
O2' G:A45 3.4 41.4 1.0
C8 G:A45 3.4 40.6 1.0
C2' G:A45 3.5 41.9 1.0
C2 G:2ZY101 3.6 38.0 1.0
C4 G:2ZY101 3.6 38.0 1.0
O2 G:U42 4.0 41.9 1.0
N7 G:A45 4.0 39.9 1.0
N9 G:A45 4.0 41.0 1.0
C8 G:G16 4.0 34.7 1.0
N2 G:G46 4.1 34.0 1.0
C3 G:2ZY101 4.1 37.6 1.0
OP2 G:A45 4.1 42.2 1.0
N7 G:G16 4.2 34.2 1.0
C1' G:A45 4.4 41.9 1.0
O2' G:G15 4.4 39.0 1.0
O5' G:A45 4.5 43.0 1.0
O G:HOH222 4.5 71.4 1.0
C2 G:U42 4.7 40.6 1.0
F7 G:2ZY101 4.7 38.1 1.0
N3 G:U42 4.8 39.4 1.0
C3' G:A45 4.8 43.1 1.0
C5 G:A45 4.8 39.4 1.0
N9 G:G16 4.8 35.1 1.0
N12 G:2ZY101 4.8 40.5 1.0
C4 G:A45 4.8 39.7 1.0
C10 G:2ZY101 4.9 38.4 1.0

Fluorine binding site 2 out of 5 in 7l0z

Go back to Fluorine Binding Sites List in 7l0z
Fluorine binding site 2 out of 5 in the Spinach Variant Bound to Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Spinach Variant Bound to Dfhbi-1T within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F101

b:38.1
occ:1.00
F7 G:2ZY101 0.0 38.1 1.0
C4 G:2ZY101 1.4 38.0 1.0
C5 G:2ZY101 2.4 38.4 1.0
C3 G:2ZY101 2.4 37.6 1.0
O9 G:2ZY101 2.7 38.7 1.0
O2' G:G16 3.1 39.3 1.0
C6 G:SPM102 3.2 63.3 1.0
C4 G:U42 3.3 39.0 1.0
O4 G:U42 3.4 38.2 1.0
N5 G:SPM102 3.4 63.5 1.0
C7 G:SPM102 3.4 63.2 1.0
N3 G:U42 3.5 39.4 1.0
C4 G:G16 3.6 33.6 1.0
N3 G:G16 3.6 32.9 1.0
C6 G:2ZY101 3.6 38.4 1.0
C2 G:2ZY101 3.7 38.0 1.0
N9 G:G16 3.8 35.1 1.0
C5 G:U42 3.9 39.8 1.0
C4 G:SPM102 4.0 64.6 1.0
C2' G:G16 4.1 39.4 1.0
C5 G:G16 4.1 33.6 1.0
C2 G:G16 4.1 32.6 1.0
C1 G:2ZY101 4.1 38.0 1.0
C1' G:G16 4.1 37.2 1.0
C2 G:U42 4.2 40.6 1.0
C8 G:G16 4.4 34.7 1.0
N6 G:A45 4.5 38.5 1.0
C6 G:U42 4.5 40.5 1.0
N7 G:A45 4.5 39.9 1.0
N1 G:G16 4.6 32.1 1.0
N7 G:G16 4.6 34.2 1.0
C6 G:G16 4.6 32.5 1.0
C3 G:SPM102 4.7 66.0 1.0
N1 G:U42 4.7 41.0 1.0
F8 G:2ZY101 4.7 38.6 1.0
C8 G:SPM102 4.8 64.1 1.0
O G:HOH235 4.8 66.8 1.0
N2 G:G16 4.8 32.3 1.0
O2 G:U42 4.8 41.9 1.0
C10 G:2ZY101 4.9 38.4 1.0

Fluorine binding site 3 out of 5 in 7l0z

Go back to Fluorine Binding Sites List in 7l0z
Fluorine binding site 3 out of 5 in the Spinach Variant Bound to Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Spinach Variant Bound to Dfhbi-1T within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F101

b:43.7
occ:1.00
F20 G:2ZY101 0.0 43.7 1.0
C19 G:2ZY101 1.4 42.8 1.0
F21 G:2ZY101 2.2 44.0 1.0
F22 G:2ZY101 2.2 42.4 1.0
C16 G:2ZY101 2.4 41.6 1.0
O G:HOH240 2.9 43.8 1.0
O G:HOH241 3.3 45.3 1.0
O G:HOH254 3.3 54.3 1.0
N3 G:A50 3.4 47.0 1.0
O G:HOH214 3.7 44.0 1.0
N14 G:2ZY101 3.7 40.8 1.0
C2 G:A50 3.7 47.0 1.0
C4 G:A50 4.0 46.6 1.0
O2' G:A50 4.0 42.8 1.0
N9 G:A50 4.5 46.4 1.0
N1 G:A50 4.5 46.8 1.0
C13 G:2ZY101 4.6 41.0 1.0
C15 G:2ZY101 4.6 40.2 1.0
N2 G:G51 4.6 37.1 1.0
C1' G:A50 4.6 45.4 1.0
O18 G:2ZY101 4.7 40.9 1.0
C17 G:2ZY101 4.7 41.5 1.0
C5 G:A50 4.7 46.5 1.0
C2' G:A50 4.9 44.4 1.0
C6 G:A50 5.0 46.8 1.0

Fluorine binding site 4 out of 5 in 7l0z

Go back to Fluorine Binding Sites List in 7l0z
Fluorine binding site 4 out of 5 in the Spinach Variant Bound to Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Spinach Variant Bound to Dfhbi-1T within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F101

b:44.0
occ:1.00
F21 G:2ZY101 0.0 44.0 1.0
C19 G:2ZY101 1.3 42.8 1.0
F20 G:2ZY101 2.2 43.7 1.0
F22 G:2ZY101 2.2 42.4 1.0
C16 G:2ZY101 2.3 41.6 1.0
N14 G:2ZY101 2.8 40.8 1.0
C17 G:2ZY101 3.1 41.5 1.0
C13 G:2ZY101 3.1 41.0 1.0
C2 G:A50 3.3 47.0 1.0
N1 G:A50 3.5 46.8 1.0
N3 G:A50 3.7 47.0 1.0
C15 G:2ZY101 3.9 40.2 1.0
N3 G:A45 4.0 39.4 1.0
C6 G:A50 4.0 46.8 1.0
C4 G:A50 4.2 46.6 1.0
N12 G:2ZY101 4.2 40.5 1.0
O G:HOH254 4.3 54.3 1.0
C2 G:A45 4.3 39.0 1.0
C5 G:A50 4.4 46.5 1.0
O18 G:2ZY101 4.4 40.9 1.0
C11 G:2ZY101 4.6 39.6 1.0
N6 G:A50 4.8 47.2 1.0
O G:HOH214 4.8 44.0 1.0
O G:HOH241 5.0 45.3 1.0

Fluorine binding site 5 out of 5 in 7l0z

Go back to Fluorine Binding Sites List in 7l0z
Fluorine binding site 5 out of 5 in the Spinach Variant Bound to Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Spinach Variant Bound to Dfhbi-1T within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F101

b:42.4
occ:1.00
F22 G:2ZY101 0.0 42.4 1.0
C19 G:2ZY101 1.4 42.8 1.0
F21 G:2ZY101 2.2 44.0 1.0
F20 G:2ZY101 2.2 43.7 1.0
C16 G:2ZY101 2.4 41.6 1.0
N14 G:2ZY101 2.9 40.8 1.0
O G:HOH214 3.0 44.0 1.0
O18 G:2ZY101 3.2 40.9 1.0
C15 G:2ZY101 3.2 40.2 1.0
O2 G:U22 3.3 41.5 1.0
C2 G:A45 3.4 39.0 1.0
O G:HOH241 3.5 45.3 1.0
O G:HOH254 3.7 54.3 1.0
N3 G:A45 3.8 39.4 1.0
C13 G:2ZY101 3.8 41.0 1.0
C11 G:2ZY101 4.3 39.6 1.0
C2 G:U22 4.4 40.9 1.0
N1 G:A45 4.5 38.8 1.0
N2 G:G21 4.5 39.2 1.0
C17 G:2ZY101 4.5 41.5 1.0
N12 G:2ZY101 4.5 40.5 1.0
C1' G:C23 4.6 42.7 1.0
O G:HOH240 4.7 43.8 1.0
O4' G:C23 4.7 44.2 1.0
O2 G:C23 4.9 39.5 1.0

Reference:

S.C.Y.Jeng, R.J.Trachman Iii, F.Weissenboeck, L.Truong, K.A.Link, M.D.E.Jepsen, J.R.Knutson, E.S.Andersen, A.R.Ferre-D'amare, P.J.Unrau. Fluorogenic Aptamers Resolve the Flexibility of Rna Junctions Using Orientation-Dependent Fret. Rna V. 27 433 2021.
ISSN: ESSN 1469-9001
PubMed: 33376189
DOI: 10.1261/RNA.078220.120
Page generated: Sat Jul 10 14:11:16 2021

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