Atomistry » Fluorine » PDB 6zqs-7adg » 6zxz
Atomistry »
  Fluorine »
    PDB 6zqs-7adg »
      6zxz »

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

Go back to Fluorine Binding Sites List in 6zxz
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

Go back to Fluorine Binding Sites List in 6zxz
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

Go back to Fluorine Binding Sites List in 6zxz
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

Go back to Fluorine Binding Sites List in 6zxz
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

Go back to Fluorine Binding Sites List in 6zxz
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

Go back to Fluorine Binding Sites List in 6zxz
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

Go back to Fluorine Binding Sites List in 6zxz
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

Go back to Fluorine Binding Sites List in 6zxz
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

Go back to Fluorine Binding Sites List in 6zxz
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: Fri Aug 2 05:27:21 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy