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

Protein crystallography data

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

Other elements in 7oax:

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

Chlorine Binding Sites:

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 7oax

Go back to Chlorine Binding Sites List in 7oax
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 7oax

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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 7oax

Go back to Chlorine Binding Sites List in 7oax
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

Reference:

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
Page generated: Sat Jul 10 13:09:00 2021

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