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Fluorine in PDB 6zxz: Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification

Protein crystallography data

The structure of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification, PDB code: 6zxz was solved by E.Ennifar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.97 / 2.44
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.412, 75.267, 52.981, 90.00, 105.60, 90.00
R / Rfree (%) 21.1 / 23.2

Other elements in 6zxz:

The structure of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification also contains other interesting chemical elements:

Potassium (K) 4 atoms
Sodium (Na) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification (pdb code 6zxz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification, PDB code: 6zxz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 6zxz

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Fluorine binding site 1 out of 9 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2670

b:53.9
occ:1.00
 F24 A:QSQ2670 0.0 53.9 1.0
C23 A:QSQ2670 1.4 44.6 1.0
F25 A:QSQ2670 2.2 40.6 1.0
F26 A:QSQ2670 2.3 48.3 1.0
O2' A:QSQ2670 2.3 40.9 1.0
C1' A:QSQ2670 3.0 40.2 1.0
O4' A:QSQ2670 3.0 39.6 1.0
C2' A:QSQ2670 3.1 41.2 1.0
C4' A:QSQ2670 3.2 41.2 1.0
C3' A:QSQ2670 3.6 40.3 1.0
O3' A:QSQ2670 4.0 41.7 1.0
N9 A:QSQ2670 4.5 37.1 1.0
C5' A:QSQ2670 4.5 41.7 1.0

Fluorine binding site 2 out of 9 in 6zxz

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Fluorine binding site 2 out of 9 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2670

b:40.6
occ:1.00
 F25 A:QSQ2670 0.0 40.6 1.0
C23 A:QSQ2670 1.4 44.6 1.0
F26 A:QSQ2670 2.2 48.3 1.0
O2' A:QSQ2670 2.2 40.9 1.0
F24 A:QSQ2670 2.2 53.9 1.0
C2' A:QSQ2670 3.6 41.2 1.0
C1' A:QSQ2670 4.2 40.2 1.0
O3' A:QSQ2670 4.4 41.7 1.0
C3' A:QSQ2670 4.5 40.3 1.0
C4' A:QSQ2670 4.7 41.2 1.0
O4' A:QSQ2670 4.8 39.6 1.0

Fluorine binding site 3 out of 9 in 6zxz

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Fluorine binding site 3 out of 9 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2670

b:48.3
occ:1.00
 F26 A:QSQ2670 0.0 48.3 1.0
C23 A:QSQ2670 1.4 44.6 1.0
F25 A:QSQ2670 2.2 40.6 1.0
F24 A:QSQ2670 2.3 53.9 1.0
O2' A:QSQ2670 2.3 40.9 1.0
C1' A:QSQ2670 2.9 40.2 1.0
C2' A:QSQ2670 3.1 41.2 1.0
N3 A:QSQ2670 3.8 33.1 1.0
O4' A:QSQ2670 3.8 39.6 1.0
N9 A:QSQ2670 4.0 37.1 1.0
C4 A:QSQ2670 4.2 35.1 1.0
N2 A:G2669 4.3 35.4 1.0
C3' A:QSQ2670 4.3 40.3 1.0
C4' A:QSQ2670 4.4 41.2 1.0
O2 A:C2651 4.6 28.4 1.0
O4' A:G2671 4.8 37.4 1.0
C2 A:QSQ2670 4.9 30.6 1.0
O3' A:QSQ2670 5.0 41.7 1.0

Fluorine binding site 4 out of 9 in 6zxz

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Fluorine binding site 4 out of 9 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2670

b:47.2
occ:1.00
 F24 B:QSQ2670 0.0 47.2 1.0
C23 B:QSQ2670 1.4 47.5 1.0
F25 B:QSQ2670 2.2 46.7 1.0
F26 B:QSQ2670 2.2 48.0 1.0
O2' B:QSQ2670 2.3 47.4 1.0
C2' B:QSQ2670 3.5 43.9 1.0
O5' B:G2671 4.2 45.9 1.0
O3' B:QSQ2670 4.4 43.1 1.0
C1' B:QSQ2670 4.5 40.8 1.0
C3' B:QSQ2670 4.5 41.1 1.0
O4' B:G2671 4.9 43.0 1.0
C4' B:G2671 5.0 40.0 1.0
P B:G2671 5.0 51.1 1.0

Fluorine binding site 5 out of 9 in 6zxz

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Fluorine binding site 5 out of 9 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2670

b:46.7
occ:1.00
 F25 B:QSQ2670 0.0 46.7 1.0
C23 B:QSQ2670 1.4 47.5 1.0
F24 B:QSQ2670 2.2 47.2 1.0
F26 B:QSQ2670 2.2 48.0 1.0
O2' B:QSQ2670 2.3 47.4 1.0
C2' B:QSQ2670 3.1 43.9 1.0
C1' B:QSQ2670 3.3 40.8 1.0
N3 B:QSQ2670 4.0 36.9 1.0
O4' B:QSQ2670 4.2 42.2 1.0
N9 B:QSQ2670 4.3 38.6 1.0
C4 B:QSQ2670 4.4 37.3 1.0
C3' B:QSQ2670 4.5 41.1 1.0
N2 B:G2669 4.6 35.3 1.0
C4' B:QSQ2670 4.7 42.0 1.0
O2 B:C2651 4.9 31.6 1.0
O4' B:G2671 5.0 43.0 1.0
C2 B:QSQ2670 5.0 33.5 1.0

Fluorine binding site 6 out of 9 in 6zxz

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Fluorine binding site 6 out of 9 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2670

b:48.0
occ:1.00
 F26 B:QSQ2670 0.0 48.0 1.0
C23 B:QSQ2670 1.4 47.5 1.0
F24 B:QSQ2670 2.2 47.2 1.0
F25 B:QSQ2670 2.2 46.7 1.0
O2' B:QSQ2670 2.3 47.4 1.0
C2' B:QSQ2670 2.6 43.9 1.0
O4' B:G2671 2.9 43.0 1.0
O5' B:G2671 3.3 45.9 1.0
C4' B:G2671 3.4 40.0 1.0
C1' B:QSQ2670 3.5 40.8 1.0
N3 B:QSQ2670 3.6 36.9 1.0
C1' B:G2671 3.8 36.5 1.0
C3' B:QSQ2670 3.9 41.1 1.0
C5' B:G2671 4.0 40.5 1.0
C4 B:QSQ2670 4.1 37.3 1.0
N9 B:QSQ2670 4.1 38.6 1.0
O3' B:QSQ2670 4.2 43.1 1.0
C2 B:QSQ2670 4.5 33.5 1.0
P B:G2671 4.5 51.1 1.0
O2' B:G2671 4.5 35.4 1.0
C2' B:G2671 4.7 38.1 1.0
O4' B:QSQ2670 4.7 42.2 1.0
C3' B:G2671 4.7 40.4 1.0
N9 B:G2671 4.8 34.2 1.0
C4' B:QSQ2670 4.8 42.0 1.0

Fluorine binding site 7 out of 9 in 6zxz

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Fluorine binding site 7 out of 9 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2670

b:44.0
occ:1.00
 F24 C:QSQ2670 0.0 44.0 1.0
C23 C:QSQ2670 1.4 43.2 1.0
F25 C:QSQ2670 2.2 44.6 1.0
F26 C:QSQ2670 2.2 41.4 1.0
O2' C:QSQ2670 2.3 42.0 1.0
C2' C:QSQ2670 2.9 39.2 1.0
O5' C:G2671 3.2 45.4 1.0
O3' C:QSQ2670 3.4 39.4 1.0
C4' C:G2671 3.4 38.4 1.0
O4' C:G2671 3.5 36.4 1.0
OP1 C:G2671 3.6 44.6 1.0
C5' C:G2671 3.7 39.1 1.0
P C:G2671 3.7 41.7 1.0
C3' C:QSQ2670 3.7 39.3 1.0
C1' C:QSQ2670 4.2 39.0 1.0
C1' C:G2671 4.6 34.9 1.0
C4' C:QSQ2670 4.8 39.2 1.0
C3' C:G2671 4.8 38.0 1.0
O2' C:G2671 4.9 35.7 1.0
N3 C:QSQ2670 5.0 34.5 1.0

Fluorine binding site 8 out of 9 in 6zxz

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Fluorine binding site 8 out of 9 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2670

b:44.6
occ:1.00
 F25 C:QSQ2670 0.0 44.6 1.0
C23 C:QSQ2670 1.4 43.2 1.0
F24 C:QSQ2670 2.2 44.0 1.0
F26 C:QSQ2670 2.2 41.4 1.0
O2' C:QSQ2670 2.3 42.0 1.0
C2' C:QSQ2670 2.7 39.2 1.0
N3 C:QSQ2670 3.2 34.5 1.0
C1' C:QSQ2670 3.3 39.0 1.0
O4' C:G2671 3.5 36.4 1.0
C4 C:QSQ2670 3.8 35.7 1.0
N9 C:QSQ2670 4.0 37.5 1.0
C2 C:QSQ2670 4.1 32.4 1.0
C3' C:QSQ2670 4.1 39.3 1.0
C1' C:G2671 4.2 34.9 1.0
C4' C:G2671 4.2 38.4 1.0
O5' C:G2671 4.4 45.4 1.0
O3' C:QSQ2670 4.6 39.4 1.0
O4' C:QSQ2670 4.6 39.4 1.0
O2' C:G2671 4.8 35.7 1.0
C4' C:QSQ2670 4.9 39.2 1.0
C5' C:G2671 4.9 39.1 1.0

Fluorine binding site 9 out of 9 in 6zxz

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Fluorine binding site 9 out of 9 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2670

b:41.4
occ:1.00
 F26 C:QSQ2670 0.0 41.4 1.0
C23 C:QSQ2670 1.4 43.2 1.0
F25 C:QSQ2670 2.2 44.6 1.0
F24 C:QSQ2670 2.2 44.0 1.0
O2' C:QSQ2670 2.3 42.0 1.0
C2' C:QSQ2670 3.5 39.2 1.0
C1' C:QSQ2670 4.4 39.0 1.0
C3' C:QSQ2670 4.6 39.3 1.0
O3' C:QSQ2670 4.6 39.4 1.0

Reference:

M.Himmelstoss, K.Erharter, E.Renard, E.Ennifar, C.Kreutz, R.Micura. 2'-O-Trifluoromethylated Rna - A Powerful Modification For Rna Chemistry and uc(Nmr) Spectroscopy Chem Sci 2020.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC04520A
Page generated: Tue Jul 15 18:24:18 2025

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