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Fluorine in PDB 5bjo: Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U

Protein crystallography data

The structure of Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U, PDB code: 5bjo was solved by K.D.Warner, W.Song, G.S.Filonov, S.R.Jaffrey, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.50 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.269, 55.305, 99.002, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.8

Other elements in 5bjo:

The structure of Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Potassium (K) 4 atoms
Iodine (I) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U (pdb code 5bjo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U, PDB code: 5bjo:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5bjo

Go back to Fluorine Binding Sites List in 5bjo
Fluorine binding site 1 out of 2 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:F104

b:39.0
occ:1.00
F1 Y:747104 0.0 39.0 1.0
C2 Y:747104 1.3 37.1 1.0
C3 Y:747104 2.4 35.1 1.0
C1 Y:747104 2.4 36.1 1.0
O1 Y:747104 2.9 38.7 1.0
C2' Y:A24 3.0 42.1 1.0
O Y:HOH209 3.0 42.9 1.0
O2' Y:A24 3.2 46.6 1.0
C1' E:G25 3.3 43.4 1.0
N9 Y:A24 3.3 44.4 1.0
N3 Y:A24 3.3 37.8 1.0
C4 Y:A24 3.3 39.5 1.0
C1' Y:A24 3.3 43.7 1.0
O4' Y:G25 3.4 46.2 1.0
C4 Y:747104 3.6 35.0 1.0
N9 E:G25 3.7 37.2 1.0
C Y:747104 3.7 36.7 1.0
N3 E:G25 3.8 32.9 1.0
O4' E:G25 3.8 45.9 1.0
C4 E:G25 3.9 34.8 1.0
C8 Y:G25 4.1 38.5 1.0
C8 Y:A24 4.1 40.5 1.0
C2 Y:A24 4.1 38.6 1.0
C5 Y:A24 4.1 40.6 1.0
C5 Y:747104 4.2 33.8 1.0
C3' Y:A24 4.4 44.8 1.0
O2' E:G25 4.4 44.8 1.0
C1' Y:G25 4.4 43.2 1.0
C5' Y:G25 4.4 43.9 1.0
C2' E:G25 4.4 45.7 1.0
N9 Y:G25 4.4 39.1 1.0
C4' Y:G25 4.5 46.0 1.0
C8 E:G25 4.6 35.7 1.0
N7 Y:A24 4.6 38.2 1.0
C2 E:G25 4.6 31.9 1.0
O5' Y:G25 4.7 45.2 1.0
C6 Y:747104 4.7 38.8 1.0
O4' Y:A24 4.7 50.6 1.0
F Y:747104 4.8 46.0 1.0
C5 E:G25 4.8 35.6 1.0
N7 Y:G25 4.8 35.9 1.0
C6 Y:A24 4.8 40.3 1.0
N1 Y:A24 4.8 37.1 1.0
C4' E:G25 5.0 49.0 1.0
O Y:HOH214 5.0 41.7 1.0

Fluorine binding site 2 out of 2 in 5bjo

Go back to Fluorine Binding Sites List in 5bjo
Fluorine binding site 2 out of 2 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:F104

b:46.0
occ:1.00
F Y:747104 0.0 46.0 1.0
C Y:747104 1.3 36.7 1.0
C1 Y:747104 2.3 36.1 1.0
C5 Y:747104 2.4 33.8 1.0
O1 Y:747104 2.7 38.7 1.0
N6 Y:A11 3.2 45.6 1.0
N7 Y:A11 3.4 42.4 1.0
C6 E:G25 3.5 31.3 1.0
C5 E:G25 3.6 35.6 1.0
C4 Y:747104 3.6 35.0 1.0
C2 Y:747104 3.7 37.1 1.0
O6 E:G25 3.7 32.8 1.0
N3 Y:G25 3.8 33.9 1.0
N7 E:G25 3.8 33.7 1.0
N2 E:G22 3.9 34.6 1.0
C5 Y:A11 4.0 42.6 1.0
C6 Y:A11 4.0 44.6 1.0
C1' Y:G25 4.0 43.2 1.0
N1 E:G25 4.1 31.0 1.0
C3 Y:747104 4.1 35.1 1.0
N1 E:G22 4.1 37.6 1.0
C4 Y:G25 4.2 35.4 1.0
C2 E:G22 4.2 35.6 1.0
C4 E:G25 4.2 34.8 1.0
N9 Y:G25 4.3 39.1 1.0
O4' Y:G25 4.5 46.2 1.0
C8 E:G25 4.5 35.7 1.0
C2 Y:G25 4.5 37.2 1.0
C8 Y:A11 4.5 42.1 1.0
C2 E:G25 4.7 31.9 1.0
N13 Y:747104 4.7 38.6 1.0
N9 E:G25 4.7 37.2 1.0
F1 Y:747104 4.8 39.0 1.0
O2' Y:G25 4.8 41.5 1.0
N3 E:G25 4.8 32.9 1.0
C6 Y:747104 4.9 38.8 1.0
N2 Y:G25 4.9 34.7 1.0

Reference:

K.D.Warner, L.Sjekloca, W.Song, G.S.Filonov, S.R.Jaffrey, A.R.Ferre-D'amare. A Homodimer Interface Without Base Pairs in An Rna Mimic of Red Fluorescent Protein. Nat. Chem. Biol. V. 13 1195 2017.
ISSN: ESSN 1552-4469
PubMed: 28945234
DOI: 10.1038/NCHEMBIO.2475
Page generated: Tue Jul 15 02:34:02 2025

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