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

Protein crystallography data

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

Other elements in 4r8i:

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:

Potassium (K) 5 atoms
Sodium (Na) 1 atom

Strontium Binding Sites:

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

Strontium binding site 1 out of 1 in 4r8i

Go back to Strontium Binding Sites List in 4r8i
Strontium 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 Strontium with other atoms in the Sr 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:Sr102

b:20.1
occ:1.00
OP1 B:0A12 2.3 15.7 1.0
OP1 B:0C9 2.4 16.1 1.0
OP1 B:0C11 2.5 17.2 1.0
O B:HOH213 2.5 14.6 1.0
O B:HOH206 2.5 14.1 1.0
O B:HOH215 2.6 13.0 1.0
O5' B:0C11 3.3 17.5 1.0
P B:0C11 3.5 18.4 1.0
P B:0C9 3.8 17.6 1.0
P B:0A12 3.8 16.4 1.0
NZ A:LYS19 4.3 16.4 1.0
C5' B:0A12 4.4 17.2 1.0
O2' B:0C4 4.4 19.2 1.0
OP2 B:0C11 4.5 17.9 1.0
O5' B:0C9 4.5 16.9 1.0
C5' B:0C11 4.6 17.5 1.0
O B:HOH212 4.6 20.2 1.0
C1' B:0C4 4.6 20.0 1.0
OP2 B:0C8 4.6 19.5 1.0
OP2 B:0C9 4.6 17.3 1.0
OP2 B:0A12 4.7 16.9 1.0
C4' B:0C11 4.7 17.1 1.0
O3' B:0U10 4.7 18.2 1.0
O5' B:0A12 4.7 16.3 1.0
O3' B:0C11 4.7 16.8 1.0
C3' B:0U10 4.7 19.1 1.0
CE A:LYS19 4.8 16.9 1.0
O B:HOH207 4.8 19.0 1.0
O2 B:0C4 4.8 19.6 1.0
O5' B:0C8 4.8 18.7 1.0
O3' B:0C8 4.8 18.1 1.0
CD A:LYS19 4.8 17.7 1.0
C3' B:0C11 4.9 17.1 1.0
O3' B:0C7 5.0 19.6 1.0
C3' B:0C8 5.0 17.6 1.0

Reference:

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
Page generated: Wed Dec 16 02:24:05 2020

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