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Potassium 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:

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

Potassium Binding Sites:

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 4r8i

Go back to Potassium Binding Sites List in 4r8i
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 4r8i

Go back to Potassium Binding Sites List in 4r8i
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 4r8i

Go back to Potassium Binding Sites List in 4r8i
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 4r8i

Go back to Potassium Binding Sites List in 4r8i
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 4r8i

Go back to Potassium Binding Sites List in 4r8i
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

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: Sun Dec 13 23:48:42 2020

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