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Potassium in PDB 5kx9: Selective Small Molecule Inhibition of the Fmn Riboswitch

Protein crystallography data

The structure of Selective Small Molecule Inhibition of the Fmn Riboswitch, PDB code: 5kx9 was solved by T.O.Fischmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.04 / 2.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.280, 71.280, 138.930, 90.00, 90.00, 120.00
R / Rfree (%) 21.6 / 25.1

Other elements in 5kx9:

The structure of Selective Small Molecule Inhibition of the Fmn Riboswitch also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Selective Small Molecule Inhibition of the Fmn Riboswitch (pdb code 5kx9). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Selective Small Molecule Inhibition of the Fmn Riboswitch, PDB code: 5kx9:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 5kx9

Go back to Potassium Binding Sites List in 5kx9
Potassium binding site 1 out of 7 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K101

b:0.6
occ:1.00
O2' X:A40 3.4 71.1 1.0
C2' X:A40 4.0 71.9 1.0
O6 X:G35 4.3 85.9 1.0
N7 X:G35 4.3 85.2 1.0
O6 X:G36 4.4 88.7 1.0
O4 X:U34 4.5 78.1 1.0
C5 X:U34 4.5 76.6 1.0
C4 X:U34 4.7 77.6 1.0
OP2 X:A40 4.8 74.0 1.0
O4 X:U37 4.9 89.4 1.0
C3' X:A40 4.9 72.9 1.0
C6 X:G35 5.0 86.1 1.0
C5 X:G35 5.0 85.5 1.0

Potassium binding site 2 out of 7 in 5kx9

Go back to Potassium Binding Sites List in 5kx9
Potassium binding site 2 out of 7 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K102

b:0.9
occ:1.00
OP2 X:A14 2.3 89.0 1.0
N7 X:G15 3.7 84.0 1.0
P X:A14 3.8 88.7 1.0
O2' X:C13 3.9 86.0 1.0
O6 X:G15 4.1 84.3 1.0
C2' X:C13 4.2 85.9 1.0
O3' X:C13 4.3 88.0 1.0
N7 X:G16 4.4 93.7 1.0
O4' X:U23 4.4 86.0 1.0
C5 X:G15 4.6 84.1 1.0
O5' X:A14 4.7 86.4 1.0
C3' X:C13 4.7 86.2 1.0
C8 X:G15 4.7 83.9 1.0
C6 X:G15 4.7 84.2 1.0
OP1 X:A14 4.7 89.2 1.0
OP2 X:G15 4.9 80.8 1.0
C4' X:U23 4.9 86.3 1.0

Potassium binding site 3 out of 7 in 5kx9

Go back to Potassium Binding Sites List in 5kx9
Potassium binding site 3 out of 7 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K103

b:0.0
occ:1.00
OP2 X:G16 3.5 91.9 1.0
OP1 X:G16 4.0 94.4 1.0
P X:G16 4.0 92.6 1.0
O3' X:G15 4.4 89.8 1.0
OP1 X:G15 4.5 80.9 1.0
C5' X:G15 4.8 82.7 1.0

Potassium binding site 4 out of 7 in 5kx9

Go back to Potassium Binding Sites List in 5kx9
Potassium binding site 4 out of 7 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K104

b:97.7
occ:1.00
N7 X:G32 4.1 67.8 1.0
O6 X:G41 4.1 76.2 1.0
O6 X:G32 4.1 68.8 1.0
C5 X:C31 4.6 65.4 1.0
C6 X:G32 4.8 68.8 1.0
C5 X:G32 4.8 68.2 1.0
N4 Y:C82 4.8 82.8 1.0
N4 X:C31 4.9 65.2 1.0

Potassium binding site 5 out of 7 in 5kx9

Go back to Potassium Binding Sites List in 5kx9
Potassium binding site 5 out of 7 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K105

b:0.7
occ:1.00
O6 Y:G91 3.9 84.5 1.0
N6 X:A22 4.1 98.3 1.0
N1 X:A22 4.5 98.5 1.0
O2' X:C25 4.7 95.5 1.0
N1 Y:A90 4.8 0.4 1.0
C6 X:A22 4.8 98.3 1.0
C6 Y:G91 4.9 83.7 1.0
C2 Y:A90 4.9 0.1 1.0

Potassium binding site 6 out of 7 in 5kx9

Go back to Potassium Binding Sites List in 5kx9
Potassium binding site 6 out of 7 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K106

b:0.6
occ:1.00
O6 X:G28 2.4 93.7 1.0
C6 X:G28 3.7 92.3 1.0
N6 X:A29 4.2 81.8 1.0
OP2 X:C25 4.5 89.6 1.0
O4 Y:U94 4.6 74.4 1.0
N1 X:G28 4.6 91.1 1.0
C5 X:G28 4.6 91.4 1.0
N3 X:C13 4.7 83.1 1.0
N7 X:G28 4.8 91.4 1.0
O2 X:C13 4.9 84.2 1.0

Potassium binding site 7 out of 7 in 5kx9

Go back to Potassium Binding Sites List in 5kx9
Potassium binding site 7 out of 7 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:K203

b:0.2
occ:1.00
O6 Y:G97 3.5 86.0 1.0
N7 Y:G97 4.0 85.2 1.0
C6 Y:G97 4.2 85.6 1.0
C5 Y:G97 4.4 85.6 1.0
O4 Y:U96 4.5 94.1 1.0
O6 Y:G98 4.5 93.9 1.0
C4 Y:U96 4.9 93.1 1.0
C5 Y:U96 5.0 92.2 1.0

Reference:

J.A.Howe, L.Xiao, T.O.Fischmann, H.Wang, H.Tang, A.Villafania, R.Zhang, C.M.Barbieri, T.Roemer. Atomic Resolution Mechanistic Studies of Ribocil: A Highly Selective Unnatural Ligand Mimic of the E. Coli Fmn Riboswitch. Rna Biol. V. 13 946 2016.
ISSN: ESSN 1555-8584
PubMed: 27485612
DOI: 10.1080/15476286.2016.1216304
Page generated: Mon Dec 14 00:01:50 2020

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