Potassium in PDB 4r8i: High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2

The structure of High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2, PDB code: 4r8i was solved by D.Oberthuer, J.Achenbach, A.Gabdulkhakov, S.Falke, K.Buchner, C.Maasch, D.Rehders, S.Klussmann, C.Betzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.01 / 2.05
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.912, 108.912, 34.812, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25

The structure of High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2 also contains other interesting chemical elements:

Strontium	(Sr)	1 atom
Sodium	(Na)	1 atom

The binding sites of Potassium atom in the High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2 (pdb code 4r8i). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2, PDB code: 4r8i:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:23.6 occ:1.00 O B:HOH283 2.4 38.9 1.0 O2' B:0U6 2.5 34.5 1.0 C2' B:0U6 3.8 34.5 1.0 O B:HOH273 4.3 24.2 1.0 O2 B:0U6 4.6 40.5 1.0 C1' B:0U6 4.6 36.1 1.0 C2 B:0U6 4.7 40.6 1.0 N1 B:0U6 4.7 39.4 1.0 OP2 B:0C7 4.8 30.2 1.0 C3' B:0U6 4.8 31.9 1.0 O B:HOH260 4.9 35.0 1.0

Potassium binding site 2 out of 5 in the High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:K104 b:19.8 occ:1.00 O B:HOH273 2.5 24.2 1.0 O B:HOH276 2.5 48.0 1.0 O B:HOH285 2.6 27.0 1.0 O2 B:0U6 2.7 40.5 1.0 C2 B:0U6 3.9 40.6 1.0 C1' B:0U6 4.5 36.1 1.0 N1 B:0U6 4.7 39.4 1.0 N3 B:0U6 4.8 40.8 1.0

Potassium binding site 3 out of 5 in the High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:K105 b:22.2 occ:1.00 O B:HOH214 2.5 26.0 1.0 O B:HOH254 2.5 29.3 1.0 O B:HOH291 2.6 25.8 1.0 O B:HOH241 2.7 32.8 1.0 O B:HOH240 2.7 32.5 1.0 OP1 B:0U37 4.2 24.2 1.0 N4 B:0C39 4.4 21.1 1.0 O B:HOH239 4.7 34.9 1.0 O B:HOH220 4.8 29.9 1.0 C5 B:0U37 4.9 23.5 1.0 OP1 B:0C36 4.9 28.5 1.0 O B:HOH224 4.9 18.5 1.0 N7 B:0G38 5.0 18.6 1.0

Potassium binding site 4 out of 5 in the High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:K106 b:30.3 occ:1.00 O B:HOH271 2.2 32.4 1.0 O B:HOH296 2.5 32.6 1.0 O B:HOH272 2.6 38.3 1.0 O B:HOH236 2.6 29.8 1.0 O6 B:0G32 2.7 21.8 1.0 O B:HOH235 2.8 25.0 1.0 O6 B:0G33 2.9 22.8 1.0 C6 B:0G32 3.6 22.7 1.0 N7 B:0G33 3.7 24.8 1.0 C6 B:0G33 3.7 23.3 1.0 N7 B:0G32 3.8 25.4 1.0 C5 B:0G33 4.0 24.2 1.0 C5 B:0G32 4.0 24.1 1.0 N4 B:0C8 4.3 19.1 1.0 OP1 B:0C4 4.4 22.0 1.0 O B:HOH234 4.5 41.3 1.0 N4 B:0C9 4.5 17.6 1.0 N1 B:0G32 4.8 21.5 1.0 OP1 B:0A3 4.8 22.4 1.0 C8 B:0G33 4.8 25.2 1.0 N1 B:0G33 4.9 22.6 1.0 C8 B:0G32 5.0 25.7 1.0

Potassium binding site 5 out of 5 in the High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:K107 b:45.1 occ:1.00 O B:HOH293 2.4 40.9 1.0 O B:HOH292 2.6 27.0 1.0 O2 B:0C13 2.6 23.0 1.0 O B:HOH229 2.6 28.0 1.0 C2 B:0C13 3.6 23.5 1.0 N3 B:0C13 3.9 22.9 1.0 O B:HOH294 4.2 31.8 1.0 N1 B:0A12 4.6 19.6 1.0 N1 B:0C13 4.8 22.9 1.0 CSE B:0U131 5.0 56.4 1.0

D.Oberthur, J.Achenbach, A.Gabdulkhakov, K.Buchner, C.Maasch, S.Falke, D.Rehders, S.Klussmann, C.Betzel. Crystal Structure of A Mirror-Image L-Rna Aptamer (Spiegelmer) in Complex with the Natural L-Protein Target CCL2. Nat Commun V. 6 6923 2015.
ISSN: ESSN 2041-1723
PubMed: 25901662
DOI: 10.1038/NCOMMS7923