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

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

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

Fluorine	(F)	9 atoms
Sodium	(Na)	4 atoms

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification, PDB code: 6zxz:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K2701 b:63.7 occ:1.00 O A:HOH2804 3.1 33.6 1.0 N7 A:G2668 3.5 32.5 1.0 OP2 A:C2667 3.5 30.5 1.0 OP2 A:G2668 3.6 33.1 1.0 C8 A:G2668 4.0 32.3 1.0 P A:C2667 4.2 32.5 1.0 O5' A:C2667 4.3 33.3 1.0 OP1 A:C2667 4.4 39.8 1.0 C5 A:G2668 4.5 32.7 1.0 O A:HOH2806 4.7 27.3 1.0 N7 A:G2669 4.7 32.7 1.0 P A:G2668 4.9 36.9 1.0 O5' A:G2668 4.9 35.3 1.0 O6 A:G2668 5.0 30.4 1.0

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K2702 b:75.0 occ:1.00 OP1 A:A2665 3.5 40.7 1.0 OP2 A:U2650 3.9 36.0 1.0 OP1 A:C2666 4.1 40.8 1.0 O3' A:A2665 4.3 35.8 1.0 C5' A:A2665 4.4 36.5 1.0 P A:C2666 4.8 33.8 1.0 P A:A2665 4.8 36.0 1.0 C4' A:A2665 4.8 35.1 1.0

Potassium binding site 3 out of 4 in the Sarcin-Ricin Loop Rna From Ecoli with A A2670-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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 B:K2701 b:60.9 occ:1.00 O B:HOH2801 3.6 32.0 1.0 OP1 B:A2665 3.6 38.5 1.0 O B:HOH2817 3.9 30.1 1.0 OP2 B:U2650 4.1 32.9 1.0 OP1 B:C2666 4.2 35.3 1.0 O3' B:A2665 4.5 36.5 1.0 O B:HOH2807 4.5 33.1 1.0 C5' B:A2665 4.6 36.7 1.0 O B:HOH2804 4.8 30.3 1.0 P B:C2666 4.9 37.1 1.0 P B:A2665 5.0 39.6 1.0

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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 C:K2701 b:77.7 occ:1.00 OP2 C:C2667 3.5 35.2 1.0 N7 C:G2668 3.8 35.6 1.0 P C:C2667 4.4 34.7 1.0 O6 C:G2668 4.4 35.3 1.0 OP2 C:G2668 4.4 36.2 1.0 C5 C:G2668 4.6 34.4 1.0 O5' C:C2667 4.6 39.0 1.0 C8 C:G2668 4.6 34.0 1.0 OP1 C:C2667 4.6 37.7 1.0 C6 C:G2668 4.8 32.6 1.0

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