Sodium in PDB 6ycq: Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna

The structure of Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna, PDB code: 6ycq was solved by I.Crespo, D.Weijers, D.R.Boer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.57 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.304, 102.784, 127.039, 90.00, 98.04, 90.00
R / Rfree (%)	17.2 / 19.9

The structure of Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Sodium atom in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna (pdb code 6ycq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna, PDB code: 6ycq:

Sodium binding site 1 out of 1 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:34.6 occ:1.00 O B:GLY137 2.3 40.0 1.0 O B:SER131 2.3 28.1 1.0 O B:SER134 2.4 35.6 1.0 O B:ASP132 2.4 28.3 1.0 O B:GLY138 2.7 35.0 1.0 C B:ASP132 2.9 31.4 1.0 O B:HOH557 2.9 43.2 1.0 C B:GLY137 3.2 40.6 1.0 C B:SER131 3.4 24.3 1.0 CA B:ASP132 3.5 28.6 1.0 C B:SER134 3.5 33.1 1.0 N B:SER134 3.6 29.8 1.0 C B:GLY138 3.6 30.8 1.0 N B:THR133 3.7 27.6 1.0 C B:THR133 3.8 34.0 1.0 CA B:GLY138 3.9 27.8 1.0 N B:GLY138 3.9 33.9 1.0 N B:ASP132 3.9 20.4 1.0 CA B:SER134 4.0 29.4 1.0 CA B:THR133 4.1 27.0 1.0 NE1 B:TRP193 4.1 20.3 1.0 O B:HOH621 4.2 32.6 1.0 N B:GLY137 4.2 43.3 1.0 CD1 B:TRP193 4.3 25.0 1.0 CA B:GLY137 4.3 45.2 1.0 O B:THR133 4.3 35.1 1.0 O B:HOH526 4.4 32.2 1.0 CB B:SER134 4.5 27.6 1.0 N B:THR135 4.6 28.8 1.0 CA B:SER131 4.7 28.1 1.0 N B:PHE139 4.8 27.2 1.0 CB B:ASP132 4.9 19.1 1.0 CA B:THR135 5.0 29.2 1.0

A.Freire-Rios, K.Tanaka, I.Crespo, E.Van Der Wijk, Y.Sizentsova, V.Levitsky, S.Lindhoud, M.Fontana, J.Hohlbein, D.R.Boer, V.Mironova, D.Weijers. Architecture of Dna Elements Mediating Arf Transcription Factor Binding and Auxin-Responsive Gene Expression in Arabidopsis . Proc.Natl.Acad.Sci.Usa V. 117 24557 2020.
ISSN: ESSN 1091-6490
PubMed: 32929017
DOI: 10.1073/PNAS.2009554117