Sodium 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:

Fluorine (F) 9 atoms
Potassium (K) 4 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 6zxz

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Sodium 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 Sodium with other atoms in the Na 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:Na2703

b:52.1
occ:1.00
OP1 A:G2648 2.5 56.4 1.0
P A:G2648 3.9 55.0 1.0
OP2 A:C2649 4.4 37.0 1.0
O5' A:G2648 4.5 47.0 1.0
C5' A:C2666 4.7 32.1 1.0
OP2 A:G2648 4.9 46.5 1.0

Sodium binding site 2 out of 4 in 6zxz

Go back to Sodium Binding Sites List in 6zxz
Sodium 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 Sodium with other atoms in the Na 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
B:Na2702

b:48.9
occ:1.00
O6 B:G2659 3.7 39.6 1.0
O6 B:G2663 3.9 32.6 1.0
OP2 B:U2656 4.4 35.6 1.0
O B:HOH2822 4.6 33.2 1.0
C6 B:G2659 4.7 35.3 1.0
N1 B:G2659 4.7 35.9 1.0
O2' B:G2655 4.7 34.4 1.0
OP1 B:A2662 4.7 36.2 1.0
O6 B:G2664 4.8 33.8 1.0
OP2 B:A2662 4.8 35.5 1.0
N7 B:G2663 4.9 34.8 1.0
C6 B:G2663 4.9 32.9 1.0

Sodium binding site 3 out of 4 in 6zxz

Go back to Sodium Binding Sites List in 6zxz
Sodium 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 Sodium with other atoms in the Na 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
C:Na2702

b:63.4
occ:1.00
OP2 C:C2649 4.1 43.5 1.0
OP1 C:G2648 4.2 56.2 1.0
P C:G2648 4.3 65.3 1.0
OP1 C:C2666 4.6 44.2 1.0
C5' C:C2666 4.9 36.5 1.0
O5' C:G2648 5.0 51.2 1.0

Sodium binding site 4 out of 4 in 6zxz

Go back to Sodium Binding Sites List in 6zxz
Sodium 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 Sodium with other atoms in the Na 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:Na2703

b:47.6
occ:1.00
N2 C:G2663 4.0 34.4 1.0
OP1 A:G2673 4.0 48.8 1.0
N3 C:G2663 4.2 32.3 1.0
O2' C:G2663 4.2 38.7 1.0
O3' A:U2672 4.3 40.6 1.0
C2 C:G2663 4.6 34.9 1.0
N6 C:A2662 4.6 31.6 1.0
O4' C:G2664 4.7 39.4 1.0
P A:G2673 4.7 49.1 1.0
C5' A:U2672 4.7 36.8 1.0
C2' C:G2663 4.8 37.1 1.0
C4' A:U2672 4.9 38.7 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: Thu Dec 17 13:14:26 2020

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