Potassium in PDB 7oaw: Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+

Protein crystallography data

The structure of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+, PDB code: 7oaw was solved by M.Mieczkowski, V.Pena, C.Hoebartner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.44 / 2.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.071, 100.031, 113.865, 90, 90, 90
R / Rfree (%) 21.8 / 26.5

Other elements in 7oaw:

The structure of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+ also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Magnesium (Mg) 2 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+ (pdb code 7oaw). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 12 binding sites of Potassium where determined in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+, PDB code: 7oaw:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 12 in 7oaw

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Potassium binding site 1 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+


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 Chili Rna Aptamer in Complex with Dmhbi+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K102

b:93.2
occ:1.00
O6 A:G42 2.7 95.5 1.0
O6 A:G32 2.7 78.0 1.0
O6 A:G37 2.7 88.0 1.0
O6 A:G9 2.8 103.3 1.0
O6 A:G36 2.8 72.8 1.0
O6 A:G13 2.9 85.4 1.0
O6 A:G12 3.2 76.3 1.0
C6 A:G32 3.4 81.8 1.0
C6 A:G42 3.5 95.5 1.0
N1 A:G42 3.5 91.8 1.0
K A:K103 3.5 84.3 1.0
N1 A:G32 3.5 81.3 1.0
C6 A:G9 3.5 90.7 1.0
C6 A:G37 3.6 88.6 1.0
O6 A:G41 3.6 83.5 1.0
N1 A:G13 3.6 84.3 1.0
C6 A:G36 3.6 76.7 1.0
C6 A:G13 3.6 84.7 1.0
N1 A:G9 3.7 88.7 1.0
N1 A:G36 3.8 77.8 1.0
N1 A:G37 3.9 86.8 1.0
C6 A:G12 4.0 75.5 1.0
N1 A:G12 4.2 74.5 1.0
O2 A:C44 4.3 90.2 1.0
C6 A:G41 4.4 80.5 1.0
C2 A:C44 4.5 88.7 1.0
N3 A:C44 4.6 91.0 1.0
N1 A:G41 4.6 78.4 1.0
C5 A:G32 4.6 80.7 1.0
C2 A:G32 4.7 86.5 1.0
C2 A:G42 4.8 85.0 1.0
C5 A:G37 4.8 87.7 1.0
C5 A:G9 4.8 82.1 1.0
C5 A:G42 4.9 96.8 1.0
C2 A:G13 4.9 74.1 1.0
C2 A:G9 4.9 84.5 1.0
C5 A:G36 4.9 76.0 1.0

Potassium binding site 2 out of 12 in 7oaw

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Potassium binding site 2 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+


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 Chili Rna Aptamer in Complex with Dmhbi+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:84.3
occ:1.00
O29 A:V6T104 2.7 80.3 1.0
O6 A:G41 2.7 83.5 1.0
O6 A:G37 2.8 88.0 1.0
O02 A:V6T104 2.8 84.6 1.0
O6 A:G15 3.0 86.3 1.0
O6 A:G32 3.0 78.0 1.0
O6 A:G13 3.3 85.4 1.0
K A:K102 3.5 93.2 1.0
C6 A:G37 3.5 88.6 1.0
C28 A:V6T104 3.5 77.6 1.0
C03 A:V6T104 3.6 76.7 1.0
N1 A:G37 3.6 86.8 1.0
C6 A:G41 3.7 80.5 1.0
C6 A:G32 3.8 81.8 1.0
N1 A:G32 3.8 81.3 1.0
C6 A:G13 3.9 84.7 1.0
N4 A:C40 3.9 94.5 1.0
C01 A:V6T104 3.9 85.8 1.0
C6 A:G15 3.9 83.4 1.0
N1 A:G13 4.0 84.3 1.0
N1 A:G41 4.1 78.4 1.0
N7 A:G15 4.6 90.1 1.0
C5 A:G15 4.6 88.4 1.0
O6 A:G42 4.7 95.5 1.0
C5 A:G37 4.8 87.7 1.0
C25 A:V6T104 4.8 76.6 1.0
C2 A:G37 4.8 80.7 1.0
C04 A:V6T104 4.9 76.2 1.0
N1 A:G15 5.0 78.8 1.0
C5 A:G41 5.0 80.6 1.0

Potassium binding site 3 out of 12 in 7oaw

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Potassium binding site 3 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+


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 Chili Rna Aptamer in Complex with Dmhbi+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K105

b:145.0
occ:1.00
O6 A:G17 3.1 97.4 1.0
O4 A:U30 3.5 101.6 1.0
OP2 A:C16 3.5 77.2 1.0
O6 A:G29 3.6 79.3 1.0
O6 A:G31 3.8 77.7 1.0
OP2 A:G15 4.0 69.1 1.0
N4 A:C18 4.1 90.8 1.0
C6 A:G17 4.1 86.0 1.0
N1 A:G31 4.3 84.9 1.0
C6 A:G31 4.4 79.5 1.0
N7 A:G17 4.4 81.8 1.0
C4 A:U30 4.5 96.3 1.0
N3 A:U30 4.6 91.0 1.0
C5 A:G17 4.7 81.2 1.0
C6 A:G29 4.7 76.1 1.0
C5 A:C16 4.8 88.5 1.0
P A:C16 5.0 76.5 1.0

Potassium binding site 4 out of 12 in 7oaw

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Potassium binding site 4 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K102

b:85.5
occ:1.00
O6 B:G42 2.7 101.8 1.0
O6 B:G36 2.7 77.3 1.0
O6 B:G9 2.7 82.5 1.0
O6 B:G13 2.7 82.6 1.0
O6 B:G32 2.8 67.9 1.0
O6 B:G37 2.8 97.6 1.0
O6 B:G12 3.1 66.4 1.0
N1 B:G42 3.4 94.0 1.0
K B:K103 3.4 89.4 1.0
C6 B:G42 3.4 97.1 1.0
O6 B:G41 3.4 84.1 1.0
C6 B:G37 3.5 97.9 1.0
C6 B:G9 3.5 80.5 1.0
C6 B:G36 3.6 78.9 1.0
C6 B:G32 3.6 69.1 1.0
C6 B:G13 3.6 86.6 1.0
N1 B:G9 3.7 80.9 1.0
N1 B:G13 3.7 91.2 1.0
N1 B:G36 3.8 76.6 1.0
N1 B:G37 3.8 97.0 1.0
N1 B:G32 3.8 69.1 1.0
C6 B:G12 3.9 66.5 1.0
N1 B:G12 3.9 65.7 1.0
C6 B:G41 4.2 80.1 1.0
O2 B:C44 4.3 79.5 1.0
N1 B:G41 4.5 73.6 1.0
C2 B:C44 4.6 76.4 1.0
C2 B:G42 4.7 88.4 1.0
C5 B:G37 4.7 97.4 1.0
C5 B:G9 4.8 77.8 1.0
C5 B:G32 4.8 67.5 1.0
C5 B:G42 4.8 92.7 1.0
N3 B:C44 4.8 72.8 1.0
C5 B:G36 4.9 82.6 1.0
C5 B:G13 4.9 88.7 1.0
C2 B:G9 5.0 74.0 1.0

Potassium binding site 5 out of 12 in 7oaw

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Potassium binding site 5 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K103

b:89.4
occ:1.00
O29 B:V6T104 2.7 98.2 1.0
O6 B:G37 2.7 97.6 1.0
O6 B:G41 2.8 84.1 1.0
O02 B:V6T104 2.8 89.3 1.0
O6 B:G32 2.9 67.9 1.0
O6 B:G15 3.0 73.7 1.0
O6 B:G13 3.3 82.6 1.0
K B:K102 3.4 85.5 1.0
C6 B:G37 3.4 97.9 1.0
N1 B:G37 3.5 97.0 1.0
C28 B:V6T104 3.5 94.1 1.0
C03 B:V6T104 3.6 92.9 1.0
C6 B:G32 3.7 69.1 1.0
C6 B:G41 3.8 80.1 1.0
C01 B:V6T104 3.9 87.0 1.0
N1 B:G32 3.9 69.1 1.0
C6 B:G13 4.0 86.6 1.0
C6 B:G15 4.0 74.4 1.0
N4 B:C40 4.0 90.9 1.0
N1 B:G13 4.1 91.2 1.0
N1 B:G41 4.2 73.6 1.0
N7 B:G15 4.6 89.5 1.0
C5 B:G15 4.7 84.5 1.0
C2 B:G37 4.7 93.1 1.0
C5 B:G37 4.7 97.4 1.0
C25 B:V6T104 4.8 88.7 1.0
O6 B:G42 4.8 101.8 1.0
C04 B:V6T104 4.9 92.1 1.0
C5 B:G32 5.0 67.5 1.0

Potassium binding site 6 out of 12 in 7oaw

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Potassium binding site 6 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K105

b:94.2
occ:1.00
O6 B:G17 2.9 101.8 1.0
O6 B:G29 3.3 70.0 1.0
O4 B:U30 3.3 85.8 1.0
O6 B:G31 3.4 98.4 1.0
OP2 B:C16 3.7 85.3 1.0
C6 B:G17 4.0 95.0 1.0
N4 B:C18 4.0 121.9 1.0
C6 B:G31 4.0 92.0 1.0
N1 B:G31 4.0 87.9 1.0
N7 B:G17 4.2 88.9 1.0
C4 B:U30 4.2 93.2 1.0
N3 B:U30 4.2 93.0 1.0
OP2 B:G15 4.2 64.5 1.0
C6 B:G29 4.4 78.0 1.0
C5 B:C16 4.4 80.5 1.0
C5 B:G17 4.4 89.0 1.0
N4 B:C16 4.8 80.1 1.0

Potassium binding site 7 out of 12 in 7oaw

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Potassium binding site 7 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K103

b:83.0
occ:1.00
O6 C:G42 2.7 93.7 1.0
O6 C:G37 2.8 103.6 1.0
O6 C:G32 2.8 78.2 1.0
O6 C:G13 2.8 81.6 1.0
O6 C:G9 2.8 85.0 1.0
O6 C:G36 2.9 94.3 1.0
O6 C:G12 3.2 67.1 1.0
O6 C:G41 3.4 101.3 1.0
C6 C:G37 3.5 100.8 1.0
C6 C:G32 3.5 76.7 1.0
K C:K104 3.5 81.0 1.0
C6 C:G42 3.6 91.4 1.0
N1 C:G32 3.6 74.9 1.0
C6 C:G13 3.6 88.2 1.0
C6 C:G9 3.6 81.7 1.0
C6 C:G36 3.6 96.3 1.0
N1 C:G42 3.6 90.0 1.0
N1 C:G13 3.7 90.2 1.0
N1 C:G36 3.7 97.2 1.0
N1 C:G37 3.8 96.1 1.0
N1 C:G9 3.9 80.6 1.0
C6 C:G12 4.1 70.3 1.0
N1 C:G12 4.2 71.3 1.0
C6 C:G41 4.2 94.0 1.0
N1 C:G41 4.4 88.0 1.0
C5 C:G37 4.6 97.0 1.0
O2 C:C44 4.7 88.3 1.0
C2 C:C44 4.7 88.9 1.0
C5 C:G32 4.8 74.6 1.0
C2 C:G32 4.8 76.2 1.0
C5 C:G9 4.9 82.2 1.0
C5 C:G36 4.9 96.8 1.0
N3 C:C44 4.9 85.6 1.0
C2 C:G42 4.9 92.3 1.0
C2 C:G37 5.0 87.7 1.0
C5 C:G42 5.0 93.2 1.0
C2 C:G13 5.0 86.1 1.0
C2 C:G36 5.0 95.1 1.0
C5 C:G13 5.0 90.3 1.0

Potassium binding site 8 out of 12 in 7oaw

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Potassium binding site 8 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K104

b:81.0
occ:1.00
O29 C:V6T105 2.7 90.9 1.0
O6 C:G15 2.7 91.7 1.0
O6 C:G37 2.8 103.6 1.0
O6 C:G41 2.8 101.3 1.0
O02 C:V6T105 3.0 100.6 1.0
O6 C:G13 3.3 81.6 1.0
O6 C:G32 3.3 78.2 1.0
C6 C:G37 3.5 100.8 1.0
K C:K103 3.5 83.0 1.0
N1 C:G37 3.5 96.1 1.0
C28 C:V6T105 3.6 90.6 1.0
C6 C:G41 3.7 94.0 1.0
C6 C:G15 3.7 90.3 1.0
C03 C:V6T105 3.7 94.6 1.0
N4 C:C40 3.8 96.7 1.0
N1 C:G41 3.8 88.0 1.0
C6 C:G13 4.0 88.2 1.0
C6 C:G32 4.0 76.7 1.0
N1 C:G32 4.1 74.9 1.0
C01 C:V6T105 4.1 100.0 1.0
N1 C:G13 4.2 90.2 1.0
N7 C:G15 4.3 89.9 1.0
C5 C:G15 4.3 89.2 1.0
N1 C:G15 4.7 91.2 1.0
C2 C:G37 4.7 87.7 1.0
C5 C:G37 4.8 97.0 1.0
C25 C:V6T105 4.8 88.5 1.0
O6 C:G42 4.9 93.7 1.0
C5 C:G41 5.0 87.3 1.0

Potassium binding site 9 out of 12 in 7oaw

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Potassium binding site 9 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K106

b:138.2
occ:1.00
O6 C:G29 3.0 77.6 1.0
O4 C:U30 3.2 92.2 1.0
O6 C:G17 3.3 89.3 1.0
O6 C:G31 3.8 79.5 1.0
N4 C:C18 3.9 85.7 1.0
C4 C:U30 4.1 87.5 1.0
OP2 C:C16 4.1 93.3 1.0
C6 C:G29 4.1 75.1 1.0
OP2 C:G15 4.2 68.4 1.0
N3 C:U30 4.3 85.4 1.0
N1 C:G31 4.3 75.9 1.0
C6 C:G31 4.3 75.8 1.0
C6 C:G17 4.4 86.3 1.0
N7 C:G17 4.7 83.8 1.0
C5 C:G17 5.0 83.7 1.0
O6 C:G28 5.0 77.0 1.0

Potassium binding site 10 out of 12 in 7oaw

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Potassium binding site 10 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbi+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K101

b:87.6
occ:1.00
O6 D:G32 2.7 71.4 1.0
O6 D:G42 2.7 103.9 1.0
O6 D:G37 2.7 96.5 1.0
O6 D:G13 2.7 84.8 1.0
O6 D:G36 2.8 80.4 1.0
O6 D:G9 2.8 97.5 1.0
O6 D:G12 3.1 87.0 1.0
K D:K102 3.1 94.4 1.0
C6 D:G36 3.5 84.3 1.0
C6 D:G13 3.5 81.2 1.0
O6 D:G41 3.5 89.0 1.0
N1 D:G13 3.6 82.1 1.0
C6 D:G9 3.6 85.9 1.0
C6 D:G37 3.6 96.6 1.0
C6 D:G32 3.6 77.9 1.0
C6 D:G42 3.6 100.4 1.0
N1 D:G36 3.7 83.7 1.0
N1 D:G42 3.8 96.6 1.0
N1 D:G9 3.8 79.7 1.0
N1 D:G37 3.9 94.8 1.0
N1 D:G32 3.9 80.2 1.0
C6 D:G12 4.0 86.2 1.0
N1 D:G12 4.1 91.9 1.0
C6 D:G41 4.3 85.4 1.0
N1 D:G41 4.5 73.8 1.0
O2 D:C44 4.6 95.0 1.0
C5 D:G36 4.7 90.8 1.0
C2 D:C44 4.8 86.1 1.0
C5 D:G9 4.8 81.7 1.0
C5 D:G37 4.8 96.5 1.0
C2 D:G13 4.8 83.1 1.0
C5 D:G32 4.9 81.9 1.0
C2 D:G36 4.9 84.9 1.0
C5 D:G13 4.9 81.1 1.0

Reference:

M.Mieczkowski, C.Steinmetzger, I.Bessi, A.K.Lenz, A.Schmiedel, M.Holzapfel, C.Lambert, V.Pena, C.Hoebartner. Large Stokes Shift Fluorescence Activation in An Rna Aptamer By Intermolecular Proton Transfer to Guanine Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-23932-0
Page generated: Sat Jul 10 16:29:24 2021

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