Sodium in PDB 6gre: Crystal Structure of the Tandem DUF26 Ectodomain From the Arabidopsis Thaliana Cysteine-Rich Receptor-Like Protein PDLP5.

The structure of Crystal Structure of the Tandem DUF26 Ectodomain From the Arabidopsis Thaliana Cysteine-Rich Receptor-Like Protein PDLP5., PDB code: 6gre was solved by B.Brandt, M.Hothorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.77 / 1.29
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.760, 47.970, 62.190, 97.70, 102.72, 99.86
R / Rfree (%)	18.6 / 21

The binding sites of Sodium atom in the Crystal Structure of the Tandem DUF26 Ectodomain From the Arabidopsis Thaliana Cysteine-Rich Receptor-Like Protein PDLP5. (pdb code 6gre). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Tandem DUF26 Ectodomain From the Arabidopsis Thaliana Cysteine-Rich Receptor-Like Protein PDLP5., PDB code: 6gre:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Tandem DUF26 Ectodomain From the Arabidopsis Thaliana Cysteine-Rich Receptor-Like Protein PDLP5.


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 Tandem DUF26 Ectodomain From the Arabidopsis Thaliana Cysteine-Rich Receptor-Like Protein PDLP5. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:38.4 occ:1.00 OD2 A:ASP92 2.0 35.8 1.0 OH A:TYR177 2.6 21.6 1.0 CG A:ASP92 2.9 30.1 1.0 OD1 A:ASP92 3.3 29.3 1.0 CG2 A:THR179 3.6 15.1 1.0 CZ A:TYR177 3.6 18.3 1.0 NH2 A:ARG90 3.7 33.6 1.0 CE2 A:TYR177 3.8 19.6 1.0 NE A:ARG90 3.9 31.7 1.0 CZ A:ARG90 4.1 33.1 1.0 CB A:ASP92 4.2 28.3 1.0 CB A:THR179 4.6 14.2 1.0 OG1 A:THR179 4.8 17.6 1.0 CD A:ARG90 4.8 29.3 1.0 CE1 A:TYR177 4.9 18.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Tandem DUF26 Ectodomain From the Arabidopsis Thaliana Cysteine-Rich Receptor-Like Protein PDLP5.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Tandem DUF26 Ectodomain From the Arabidopsis Thaliana Cysteine-Rich Receptor-Like Protein PDLP5. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na309 b:39.0 occ:1.00 OD2 B:ASP92 2.0 35.3 1.0 OH B:TYR177 2.6 16.7 1.0 CG B:ASP92 2.9 29.7 1.0 OD1 B:ASP92 3.2 26.0 1.0 O B:HOH459 3.2 23.4 1.0 NH2 B:ARG90 3.5 32.8 0.7 CG2 B:THR179 3.6 13.8 1.0 CZ B:TYR177 3.6 13.5 1.0 CE2 B:TYR177 3.8 13.1 1.0 NE B:ARG90 4.1 29.1 0.7 CZ B:ARG90 4.1 29.6 0.7 CB B:ASP92 4.2 26.6 1.0 CB B:THR179 4.5 12.6 1.0 NE B:ARG90 4.6 21.9 0.3 OG1 B:THR179 4.7 14.9 1.0 CE1 B:TYR177 4.9 13.9 1.0

A.Vaattovaara, B.Brandt, S.Rajaraman, O.Safronov, A.Veidenberg, M.Luklova, J.Kangasjarvi, A.Loytynoja, M.Hothorn, J.Salojarvi, M.Wrzaczek. Mechanistic Insights Into the Evolution of DUF26-Containing Proteins in Land Plants. Commun Biol V. 2 56 2019.
ISSN: ESSN 2399-3642
PubMed: 30775457
DOI: 10.1038/S42003-019-0306-9