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

Protein crystallography data

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

Other elements in 7l0z:

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

Sodium (Na) 2 atoms
Fluorine (F) 5 atoms
Magnesium (Mg) 1 atom

Potassium Binding Sites:

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

Potassium binding site 1 out of 2 in 7l0z

Go back to Potassium Binding Sites List in 7l0z
Potassium binding site 1 out of 2 in the Spinach Variant Bound to Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Spinach Variant Bound to Dfhbi-1T within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K110

b:41.7
occ:1.00
O6 G:G20 2.5 35.1 1.0
O6 G:G16 2.6 32.4 1.0
O6 G:G49 2.6 32.3 1.0
O6 G:G51 2.7 33.9 1.0
O6 G:G46 2.8 35.1 1.0
O6 G:G15 3.2 31.3 1.0
O6 G:G19 3.3 33.5 1.0
C6 G:G20 3.3 34.8 1.0
O6 G:G53 3.4 35.0 1.0
C6 G:G49 3.5 32.9 1.0
C6 G:G16 3.5 32.5 1.0
N1 G:G20 3.5 34.6 1.0
C6 G:G51 3.6 35.1 1.0
C6 G:G46 3.6 34.8 1.0
N1 G:G16 3.7 32.1 1.0
N1 G:G49 3.8 33.0 1.0
C6 G:G15 3.8 31.7 1.0
N1 G:G46 3.9 33.8 1.0
K G:K111 3.9 36.4 1.0
N1 G:G51 3.9 35.0 1.0
N1 G:G15 4.1 32.0 1.0
C6 G:G53 4.2 36.1 1.0
N1 G:G53 4.2 36.4 1.0
C6 G:G19 4.2 34.3 1.0
N1 G:G19 4.6 35.1 1.0
C5 G:G20 4.6 35.1 1.0
C5 G:G49 4.6 33.5 1.0
N1 G:G21 4.7 38.7 1.0
C5 G:G16 4.8 33.6 1.0
C5 G:G15 4.8 32.7 1.0
C5 G:G51 4.8 36.4 1.0
C2 G:G20 4.8 34.7 1.0
O6 G:G21 4.9 38.9 1.0
O18 G:2ZY101 4.9 40.9 1.0
C6 G:G21 4.9 38.7 1.0
C5 G:G46 4.9 35.6 1.0

Potassium binding site 2 out of 2 in 7l0z

Go back to Potassium Binding Sites List in 7l0z
Potassium binding site 2 out of 2 in the Spinach Variant Bound to Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Spinach Variant Bound to Dfhbi-1T within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K111

b:36.4
occ:1.00
O6 G:G15 2.7 31.3 1.0
O2 G:U54 2.8 33.3 1.0
O6 G:G55 2.9 31.9 1.0
O6 G:G49 2.9 32.3 1.0
O G:HOH234 3.0 34.0 1.0
O6 G:G19 3.0 33.5 1.0
O6 G:G53 3.0 35.0 1.0
O2' G:U54 3.1 37.7 1.0
N7 G:G55 3.5 33.3 1.0
C6 G:G53 3.6 36.1 1.0
C6 G:G55 3.6 33.0 1.0
C6 G:G49 3.7 32.9 1.0
C6 G:G15 3.7 31.7 1.0
C6 G:G19 3.8 34.3 1.0
C5 G:G55 3.9 33.2 1.0
N1 G:G53 3.9 36.4 1.0
N1 G:G49 3.9 33.0 1.0
K G:K110 3.9 41.7 1.0
N1 G:G19 3.9 35.1 1.0
C2' G:U54 4.0 37.6 1.0
N1 G:G15 4.0 32.0 1.0
C2 G:U54 4.0 35.1 1.0
C1' G:U54 4.3 36.6 1.0
C5 G:G53 4.6 37.1 1.0
C8 G:G55 4.7 34.7 1.0
N4 G:C18 4.7 35.1 1.0
N1 G:U54 4.7 35.6 1.0
N3 G:U47 4.8 32.5 1.0
C5 G:G49 4.8 33.5 1.0
N1 G:G55 4.9 34.2 1.0
C5 G:G15 5.0 32.7 1.0

Reference:

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
Page generated: Sat Jul 10 16:27:16 2021

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