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Potassium in PDB 5bjp: Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak

Protein crystallography data

The structure of Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak, PDB code: 5bjp was solved by K.D.Warner, W.Song, G.S.Filonov, 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) 49.34 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.642, 55.438, 98.676, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.9

Other elements in 5bjp:

The structure of Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Magnesium (Mg) 2 atoms
Iridium (Ir) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak (pdb code 5bjp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak, PDB code: 5bjp:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5bjp

Go back to Potassium Binding Sites List in 5bjp
Potassium binding site 1 out of 4 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak


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 Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K102

b:30.2
occ:1.00
O6 E:G16 2.7 29.6 1.0
O E:HOH202 2.8 37.0 1.0
O6 E:G23 2.9 29.4 1.0
O E:HOH204 2.9 33.9 1.0
O6 E:G26 2.9 32.2 1.0
O6 E:G13 3.1 28.6 1.0
O2 E:U17 3.1 36.8 1.0
K E:K103 3.6 30.4 1.0
C6 E:G16 3.7 30.4 1.0
C6 E:G23 3.8 30.7 1.0
C2 E:U17 3.8 36.5 1.0
C6 E:G26 3.8 29.7 1.0
C6 E:G13 3.9 28.8 1.0
O E:HOH206 3.9 32.1 1.0
N3 E:U17 3.9 35.6 1.0
N1 E:G16 4.0 27.8 1.0
N1 E:G23 4.1 29.3 1.0
N1 E:G13 4.1 27.5 1.0
N1 E:G26 4.1 31.0 1.0
C2 E:A21 4.2 35.3 1.0
N1 E:A21 4.2 32.1 1.0
C2 E:A10 4.3 27.4 1.0
N1 E:A10 4.5 28.7 1.0
N3 E:U27 4.7 31.3 1.0
C5 E:G16 4.9 29.2 1.0

Potassium binding site 2 out of 4 in 5bjp

Go back to Potassium Binding Sites List in 5bjp
Potassium binding site 2 out of 4 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak


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 Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K103

b:30.4
occ:1.00
O6 E:G15 2.6 30.8 1.0
O6 E:G25 2.7 22.0 1.0
O6 E:G22 2.7 34.2 1.0
O6 E:G12 2.7 25.4 1.0
O6 E:G13 2.9 28.6 1.0
O6 E:G16 2.9 29.6 1.0
O6 E:G26 3.0 32.2 1.0
O6 E:G23 3.1 29.4 1.0
C6 E:G12 3.5 24.7 1.0
K E:K102 3.6 30.2 1.0
C6 E:G16 3.6 30.4 1.0
C6 E:G25 3.6 22.9 1.0
C6 E:G15 3.6 28.5 1.0
C6 E:G22 3.7 27.8 1.0
N1 E:G12 3.7 27.2 1.0
C6 E:G23 3.8 30.7 1.0
N6 Y:A11 3.8 30.3 1.0
C6 E:G13 3.8 28.8 1.0
C6 E:G26 3.8 29.7 1.0
N1 E:G16 3.8 27.8 1.0
N1 E:G25 3.9 24.9 1.0
N1 E:G22 3.9 24.4 1.0
N1 E:G15 4.0 30.2 1.0
N1 E:G13 4.0 27.5 1.0
N1 E:G23 4.0 29.3 1.0
N1 E:G26 4.1 31.0 1.0
C6 Y:A11 4.5 30.5 1.0
C5 E:G12 4.8 25.7 1.0
C5 E:G16 4.8 29.2 1.0
C5 E:G23 4.9 32.6 1.0
C5 E:G15 4.9 27.1 1.0
N1 Y:A11 4.9 29.4 1.0
C5 E:G25 4.9 24.3 1.0
C2 E:G12 5.0 26.9 1.0

Potassium binding site 3 out of 4 in 5bjp

Go back to Potassium Binding Sites List in 5bjp
Potassium binding site 3 out of 4 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak


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 Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:K102

b:28.7
occ:1.00
O6 Y:G15 2.7 26.9 1.0
O6 Y:G22 2.7 30.5 1.0
O6 Y:G25 2.8 28.5 1.0
O6 Y:G12 2.8 25.2 1.0
O6 Y:G16 2.8 28.9 1.0
O6 Y:G23 2.9 25.4 1.0
O6 Y:G13 3.0 34.4 1.0
O6 Y:G26 3.1 29.3 1.0
K Y:K103 3.5 31.4 1.0
C6 Y:G16 3.6 27.6 1.0
C6 Y:G12 3.6 24.9 1.0
C6 Y:G23 3.7 26.7 1.0
C6 Y:G25 3.7 28.0 1.0
C6 Y:G15 3.7 28.1 1.0
C6 Y:G22 3.7 27.9 1.0
C6 Y:G13 3.8 28.4 1.0
N1 Y:G12 3.8 23.5 1.0
N1 Y:G16 3.8 27.0 1.0
C6 Y:G26 3.9 25.1 1.0
N1 Y:G13 3.9 26.4 1.0
N1 Y:G25 3.9 27.0 1.0
N1 Y:G23 4.0 26.0 1.0
N1 Y:G22 4.0 27.8 1.0
N1 Y:G26 4.0 24.8 1.0
N1 Y:G15 4.1 30.2 1.0
C16 Y:747104 4.6 26.6 1.0
N15 Y:747104 4.6 24.9 1.0
C5 Y:G23 4.8 25.6 1.0
C5 Y:G16 4.8 27.0 1.0
C5 Y:G12 4.9 29.3 1.0
C10 Y:747104 4.9 25.9 1.0
C12 Y:747104 4.9 26.2 1.0
C5 Y:G15 5.0 28.1 1.0
C5 Y:G25 5.0 27.5 1.0

Potassium binding site 4 out of 4 in 5bjp

Go back to Potassium Binding Sites List in 5bjp
Potassium binding site 4 out of 4 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak


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 Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:K103

b:31.4
occ:1.00
O6 Y:G23 2.7 25.4 1.0
O6 Y:G16 2.8 28.9 1.0
O Y:HOH203 2.9 25.9 1.0
O6 Y:G26 2.9 29.3 1.0
O Y:HOH205 3.0 28.3 1.0
O2 Y:U17 3.0 39.1 1.0
O6 Y:G13 3.1 34.4 1.0
K Y:K102 3.5 28.7 1.0
C6 Y:G23 3.7 26.7 1.0
C6 Y:G16 3.7 27.6 1.0
C6 Y:G26 3.8 25.1 1.0
N1 Y:G23 3.9 26.0 1.0
C6 Y:G13 3.9 28.4 1.0
C2 Y:A21 3.9 35.2 1.0
C2 Y:U17 3.9 34.5 1.0
N1 Y:A21 3.9 34.2 1.0
N1 Y:G13 3.9 26.4 1.0
N1 Y:G16 4.1 27.0 1.0
O Y:HOH204 4.1 37.4 1.0
N3 Y:U17 4.2 34.6 1.0
N1 Y:G26 4.2 24.8 1.0
C2 Y:A10 4.4 33.1 1.0
N1 Y:A10 4.7 30.8 1.0
N3 Y:U27 4.7 33.5 1.0
O2 Y:U27 4.9 30.6 1.0
N3 Y:A21 4.9 33.6 1.0
C5 Y:G23 5.0 25.6 1.0
C5 Y:G16 5.0 27.0 1.0

Reference:

K.D.Warner, L.Sjekloca, W.Song, G.S.Filonov, S.R.Jaffrey, A.R.Ferre-D'amare. A Homodimer Interface Without Base Pairs in An Rna Mimic of Red Fluorescent Protein. Nat. Chem. Biol. V. 13 1195 2017.
ISSN: ESSN 1552-4469
PubMed: 28945234
DOI: 10.1038/NCHEMBIO.2475
Page generated: Sun Dec 13 23:54:57 2020

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