Sodium 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
Potassium	(K)	5 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the High Resolution Structure of A Mirror-Image Rna Oligonucleotide Aptamer in Complex with the Chemokine CCL2, PDB code: 4r8i:

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na101 b:23.9 occ:1.00 O B:HOH248 2.1 47.7 1.0 O B:HOH221 2.5 30.0 1.0 O4 B:0U131 2.5 43.0 1.0 O B:HOH245 2.6 28.5 1.0 O B:HOH246 2.8 34.4 1.0 C4 B:0U131 3.8 44.3 1.0 C5 B:0C4 4.2 22.0 1.0 O B:HOH249 4.3 37.1 1.0 C5 B:0U131 4.5 42.8 1.0 N4 B:0C4 4.6 23.1 1.0 O6 B:0G30 4.7 25.8 1.0 N3 B:0U131 4.7 41.4 1.0 N7 B:0G30 4.8 29.0 1.0 C4 B:0C4 4.8 21.8 1.0 O B:HOH232 4.9 22.1 1.0 O B:HOH243 4.9 35.8 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