Chlorine in PDB 7oax: Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+

The structure of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+, PDB code: 7oax was solved by M.Mieczkowski, V.Pena, C.Hoebartner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.97 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.324, 100.352, 113.294, 90, 90, 90
R / Rfree (%)	20.2 / 23.7

The structure of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+ also contains other interesting chemical elements:

Potassium	(K)	12 atoms
Magnesium	(Mg)	1 atom

The binding sites of Chlorine atom in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+ (pdb code 7oax). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+, PDB code: 7oax:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl105 b:95.7 occ:1.00 N2 A:G17 3.5 54.5 1.0 N9 A:G39 3.6 70.2 1.0 C8 A:G39 3.6 68.8 1.0 C1' A:G39 3.8 70.0 1.0 O4' A:G39 3.9 72.8 1.0 C4 A:G39 4.1 69.6 1.0 N7 A:G39 4.1 70.6 1.0 C5 A:G39 4.4 67.5 1.0 C1' A:C18 4.5 66.5 1.0 C2 A:G17 4.6 54.7 1.0 O4' A:C18 4.6 70.2 1.0 N3 A:G17 4.7 61.2 1.0 O2' A:C18 4.7 71.3 1.0 N3 A:G39 4.8 61.5 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl104 b:74.7 occ:1.00 O6 B:G25 3.3 62.0 1.0 N10 D:SPM102 3.4 60.0 0.8 O2' B:U22 3.6 73.8 1.0 C9 D:SPM102 3.8 55.5 0.8 C5 B:U23 4.1 67.3 1.0 C6 B:U23 4.2 67.2 1.0 C6 B:G25 4.3 53.7 1.0 N7 B:G25 4.4 48.6 1.0 O2' B:U23 4.5 74.9 1.0 C4 B:U23 4.5 73.5 1.0 C11 D:SPM102 4.6 59.5 0.8 N1 B:U23 4.7 70.7 1.0 C5 B:G25 4.7 49.2 1.0 C2' B:U22 4.8 67.4 1.0 C12 D:SPM102 4.9 56.9 0.8 C2' B:U23 4.9 66.1 1.0 N3 B:U23 4.9 71.6 1.0 C1' B:U22 5.0 56.3 1.0 O4 B:U23 5.0 79.2 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl104 b:82.3 occ:1.00 O D:HOH208 2.9 50.5 1.0 N2 D:G17 3.5 68.9 1.0 N9 D:G39 4.1 56.3 1.0 C1' D:G39 4.2 56.2 1.0 O4' D:C18 4.2 69.8 1.0 C4 D:G39 4.4 54.6 1.0 N3 D:G17 4.4 61.9 1.0 C1' D:C18 4.4 64.1 1.0 C2 D:G17 4.4 62.7 1.0 C8 D:G39 4.4 55.4 1.0 O4' D:G39 4.5 58.8 1.0 N3 D:G39 4.7 62.0 1.0 O2' D:C18 4.8 66.7 1.0 C5 D:G39 4.8 52.9 1.0 N7 D:G39 4.9 55.5 1.0

M.Mieczkowski, C.Steinmetzger, I.Bessi, A.K.Lenz, A.Schmiedel, M.Holzapfel, C.Lambert, V.Pena, C.Hoebartner. Large Stokes Shift Fluorescence Activation in An Rna Aptamer By Intermolecular Proton Transfer to Guanine Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-23932-0