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Potassium in PDB 4ts2: Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions

Protein crystallography data

The structure of Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions, PDB code: 4ts2 was solved by K.D.Warner, M.C.Chen, W.Song, R.L.Strack, A.Thorn, S.R.Jaffrey, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.877, 49.399, 188.410, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.7

Other elements in 4ts2:

The structure of Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Magnesium (Mg) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions (pdb code 4ts2). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions, PDB code: 4ts2:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 4ts2

Go back to Potassium Binding Sites List in 4ts2
Potassium binding site 1 out of 3 in the Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K102

b:72.0
occ:1.00
O2 Y:U73 2.7 75.0 1.0
O2' Y:U73 2.9 80.7 1.0
O6 Y:G74 2.9 82.2 1.0
O6 X:G25 2.9 75.9 1.0
O6 Y:G68 3.0 73.9 1.0
O6 Y:G72 3.0 66.9 1.0
O6 X:G29 3.2 84.5 1.0
N7 Y:G74 3.3 67.4 1.0
K X:K103 3.4 85.4 1.0
C6 Y:G72 3.4 62.9 1.0
C6 Y:G74 3.6 72.7 1.0
N1 Y:G72 3.7 56.2 1.0
C6 Y:G68 3.7 66.1 1.0
C5 Y:G74 3.8 67.9 1.0
N1 X:G29 3.8 86.4 1.0
C2' Y:U73 3.9 77.7 1.0
C6 X:G29 3.9 89.5 1.0
C6 X:G25 3.9 78.7 1.0
C2 Y:U73 3.9 84.5 1.0
N1 Y:G68 3.9 62.0 1.0
N1 X:G25 4.2 78.2 1.0
C1' Y:U73 4.2 78.6 1.0
C5 Y:G72 4.4 62.8 1.0
C8 Y:G74 4.5 70.2 1.0
N1 Y:U73 4.6 81.6 1.0
C2 Y:G72 4.8 61.9 1.0
N4 X:C28 4.8 85.0 1.0
N1 Y:G74 4.9 81.1 1.0
C2 X:G29 4.9 84.0 1.0
N3 Y:U73 4.9 84.0 1.0
C5 Y:G68 4.9 59.0 1.0

Potassium binding site 2 out of 3 in 4ts2

Go back to Potassium Binding Sites List in 4ts2
Potassium binding site 2 out of 3 in the Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K103

b:85.4
occ:1.00
O6 Y:G68 2.5 73.9 1.0
O6 X:G26 2.7 71.9 1.0
O6 Y:G70 2.7 72.4 1.0
O6 Y:G65 2.8 62.6 1.0
O6 X:G30 2.9 83.0 1.0
O6 X:G25 2.9 75.9 1.0
O6 Y:G72 2.9 66.9 1.0
O6 X:G29 3.1 84.5 1.0
C6 Y:G68 3.3 66.1 1.0
K X:K102 3.4 72.0 1.0
N1 Y:G68 3.5 62.0 1.0
C6 X:G26 3.5 74.8 1.0
C6 X:G25 3.6 78.7 1.0
C6 Y:G70 3.6 71.5 1.0
C6 X:G30 3.7 88.0 1.0
C6 Y:G65 3.7 67.2 1.0
N1 X:G26 3.8 75.7 1.0
C6 Y:G72 3.9 62.9 1.0
N1 X:G30 3.9 83.0 1.0
N1 X:G25 4.0 78.2 1.0
N1 Y:G72 4.0 56.2 1.0
C6 X:G29 4.0 89.5 1.0
N1 Y:G65 4.0 64.3 1.0
N1 Y:G70 4.1 72.5 1.0
N1 X:G29 4.2 86.4 1.0
C5 Y:G68 4.6 59.0 1.0
C5 X:G25 4.7 75.2 1.0
C2 Y:G68 4.7 64.7 1.0
C5 Y:G70 4.7 68.2 1.0
C5 X:G26 4.8 74.0 1.0
C5 X:G30 4.8 86.0 1.0
O2 Y:U73 4.9 75.0 1.0
C5 Y:G65 4.9 63.9 1.0

Potassium binding site 3 out of 3 in 4ts2

Go back to Potassium Binding Sites List in 4ts2
Potassium binding site 3 out of 3 in the Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:K102

b:0.8
occ:1.00
OP2 X:A23 3.8 73.1 1.0
O4 Y:U73 4.4 94.8 1.0
OP2 Y:G68 4.6 70.7 1.0

Reference:

K.D.Warner, M.C.Chen, W.Song, R.L.Strack, A.Thorn, S.R.Jaffrey, A.R.Ferre-D'amare. Structural Basis For Activity of Highly Efficient Rna Mimics of Green Fluorescent Protein. Nat.Struct.Mol.Biol. V. 21 658 2014.
ISSN: ESSN 1545-9985
PubMed: 25026079
DOI: 10.1038/NSMB.2865
Page generated: Mon Aug 12 12:11:23 2024

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