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Iodine in PDB 5uza: Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor)

Protein crystallography data

The structure of Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor), PDB code: 5uza was solved by Y.Liu, J.R.Stagno, Y.-X.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.61 / 2.22
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 48.985, 151.575, 24.735, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.1

Other elements in 5uza:

The structure of Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor) (pdb code 5uza). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor), PDB code: 5uza:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 5uza

Go back to Iodine Binding Sites List in 5uza
Iodine binding site 1 out of 2 in the Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor) within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I28

b:31.9
occ:1.00
I5 X:IU28 0.0 31.9 1.0
C5 X:IU28 2.1 30.7 1.0
C4 X:IU28 3.1 27.3 1.0
C6 X:IU28 3.1 33.5 1.0
H6 X:IU28 3.2 40.3 1.0
O4 X:IU28 3.2 26.2 1.0
OP2 X:IU28 3.4 28.0 1.0
H3' X:C27 3.4 29.7 1.0
C5 X:C27 3.8 22.1 1.0
C6 X:C27 3.9 22.6 1.0
H5 X:C27 3.9 26.5 1.0
H6 X:C27 4.1 27.1 1.0
C4 X:C27 4.2 21.6 1.0
H2' X:C27 4.3 27.2 1.0
N1 X:C27 4.3 21.8 1.0
C3' X:C27 4.4 24.7 1.0
O5' X:C27 4.4 21.8 1.0
N3 X:IU28 4.5 27.3 1.0
N1 X:IU28 4.5 33.5 1.0
OP2 X:C27 4.6 24.5 1.0
P X:IU28 4.6 29.6 1.0
O5' X:IU28 4.6 30.9 1.0
N3 X:C27 4.6 21.0 1.0
C2 X:C27 4.7 21.7 1.0
N4 X:C27 4.8 22.6 1.0
C2' X:C27 4.8 22.6 1.0
H41 X:C27 4.9 27.2 1.0

Iodine binding site 2 out of 2 in 5uza

Go back to Iodine Binding Sites List in 5uza
Iodine binding site 2 out of 2 in the Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor) within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I31

b:39.4
occ:1.00
I5 X:IU31 0.0 39.4 1.0
C5 X:IU31 2.1 32.7 1.0
C4 X:IU31 3.1 28.8 1.0
C6 X:IU31 3.1 31.8 1.0
H6 X:IU31 3.2 38.2 1.0
O4 X:IU31 3.2 27.9 1.0
H3' X:A30 3.3 43.8 1.0
H8 X:A30 3.5 35.1 1.0
OP2 X:IU31 3.6 36.0 1.0
C8 X:A30 3.7 29.2 1.0
O X:HOH216 3.7 36.6 1.0
H5'' X:A30 3.8 42.2 1.0
N7 X:A30 3.8 27.7 1.0
C3' X:A30 4.2 36.4 1.0
H5' X:A30 4.4 42.2 1.0
N9 X:A30 4.4 29.5 1.0
C5' X:A30 4.4 35.1 1.0
O X:HOH202 4.5 46.3 1.0
O X:HOH208 4.5 48.1 1.0
N3 X:IU31 4.5 27.6 1.0
N1 X:IU31 4.5 31.1 1.0
C5 X:A30 4.6 28.4 1.0
P X:IU31 4.7 38.5 1.0
O5' X:IU31 4.8 38.2 1.0
C4' X:A30 4.8 34.4 1.0
H2' X:A30 4.8 39.1 1.0
C4 X:A30 4.9 29.7 1.0
O4' X:A30 5.0 31.9 1.0
O3' X:A30 5.0 39.2 1.0

Reference:

Y.Liu, E.Holmstrom, P.Yu, K.Tan, X.Zuo, D.J.Nesbitt, R.Sousa, J.R.Stagno, Y.X.Wang. Incorporation of Isotopic, Fluorescent, and Heavy-Atom-Modified Nucleotides Into Rnas By Position-Selective Labeling of Rna. Nat Protoc V. 13 987 2018.
ISSN: ESSN 1750-2799
PubMed: 29651055
DOI: 10.1038/NPROT.2018.002
Page generated: Sun Dec 13 19:41:26 2020

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