Atomistry » Sodium » PDB 6zl4-7a2n » 6zxz
Atomistry »
  Sodium »
    PDB 6zl4-7a2n »
      6zxz »

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

Go back to Sodium Binding Sites List in 6zxz
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: Tue Oct 8 15:43:00 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy