Sodium in PDB 7l0z: Spinach Variant Bound to Dfhbi-1T

The structure of Spinach Variant Bound to Dfhbi-1T, PDB code: 7l0z was solved by L.Truong, R.J.Trachman, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.26 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.564, 48.692, 30.612, 90, 91.36, 90
R / Rfree (%)	19.6 / 23.2

The structure of Spinach Variant Bound to Dfhbi-1T also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Fluorine	(F)	5 atoms
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the Spinach Variant Bound to Dfhbi-1T (pdb code 7l0z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Spinach Variant Bound to Dfhbi-1T, PDB code: 7l0z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Spinach Variant Bound to Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Spinach Variant Bound to Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ G:Na108 b:53.7 occ:1.00 OP2 G:G19 2.4 37.7 1.0 O G:HOH211 2.6 49.7 1.0 O G:HOH235 3.1 66.8 1.0 P G:G19 3.7 40.0 1.0 C3' G:C18 3.7 40.5 1.0 C8 G:G19 3.7 36.2 1.0 N2 G:G15 3.8 34.1 1.0 C5' G:G19 3.8 38.7 1.0 C5' G:U17 3.9 54.2 1.0 O5' G:G19 4.1 39.7 1.0 N7 G:G19 4.2 35.7 1.0 N3 G:G16 4.2 32.9 1.0 O3' G:C18 4.2 40.9 1.0 C6 G:C18 4.2 37.0 1.0 C2' G:C18 4.2 39.2 1.0 O5' G:C18 4.2 48.0 1.0 O4' G:G16 4.3 38.4 1.0 OP1 G:C18 4.4 50.6 1.0 C1' G:G16 4.4 37.2 1.0 C4' G:U17 4.4 57.7 1.0 N1 G:C18 4.5 37.5 1.0 C5 G:C18 4.5 36.0 1.0 O4' G:G19 4.6 38.8 1.0 O3' G:G16 4.7 44.9 1.0 C4' G:G16 4.8 40.5 1.0 C4' G:G19 4.8 39.1 1.0 C4 G:G16 4.9 33.6 1.0 C2 G:G16 4.9 32.6 1.0 C1' G:C18 4.9 39.4 1.0 N2 G:G16 4.9 32.3 1.0 C4' G:C18 4.9 42.9 1.0 N9 G:G19 4.9 36.5 1.0

Sodium binding site 2 out of 2 in the Spinach Variant Bound to Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Spinach Variant Bound to Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ G:Na109 b:90.6 occ:0.50 O2' G:A32 2.4 75.8 1.0 N7 G:G34 2.6 93.0 1.0 C8 G:G34 3.2 91.9 1.0 O3' G:A32 3.4 86.2 1.0 C2' G:A32 3.6 78.7 1.0 C5 G:G34 3.8 90.8 1.0 C1' G:A32 4.0 80.7 1.0 C3' G:A32 4.1 82.3 1.0 OP1 G:C33 4.2 91.4 1.0 C5' G:C33 4.3 90.2 1.0 O6 G:G34 4.3 90.2 1.0 P G:C33 4.4 90.3 1.0 C6 G:G34 4.4 89.4 1.0 N9 G:G34 4.5 89.8 1.0 O5' G:C33 4.7 90.2 1.0 C4 G:G34 4.8 89.0 1.0 N9 G:A32 4.9 78.9 1.0

S.C.Y.Jeng, R.J.Trachman Iii, F.Weissenboeck, L.Truong, K.A.Link, M.D.E.Jepsen, J.R.Knutson, E.S.Andersen, A.R.Ferre-D'amare, P.J.Unrau. Fluorogenic Aptamers Resolve the Flexibility of Rna Junctions Using Orientation-Dependent Fret. Rna V. 27 433 2021.
ISSN: ESSN 1469-9001
PubMed: 33376189
DOI: 10.1261/RNA.078220.120