Sodium in PDB 7vmf: Crystal Structure of Arabidopsis Thaliana HDT2

The structure of Crystal Structure of Arabidopsis Thaliana HDT2, PDB code: 7vmf was solved by A.Kumar, R.C.Bobde, D.Vasudevan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.77 / 1.32
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	53.106, 96.221, 196.299, 90, 90, 90
R / Rfree (%)	16 / 18.9

The binding sites of Sodium atom in the Crystal Structure of Arabidopsis Thaliana HDT2 (pdb code 7vmf). 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 Arabidopsis Thaliana HDT2, PDB code: 7vmf:

Sodium binding site 1 out of 1 in the Crystal Structure of Arabidopsis Thaliana HDT2


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 Arabidopsis Thaliana HDT2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:67.8 occ:1.00 OD1 D:ASN95 2.6 75.9 1.0 CG D:ASN95 3.6 67.6 1.0 CE C:MET1 3.6 52.7 1.0 O D:PRO94 3.7 42.1 1.0 CB D:ASN95 3.9 56.4 1.0 CD1 D:LEU23 4.0 31.5 1.0 C D:PRO94 4.8 40.0 1.0 ND2 D:ASN95 4.8 76.8 1.0 CA D:ASN95 4.8 51.5 1.0 C D:ASN95 4.9 54.5 1.0 CG C:MET1 4.9 39.8 1.0 SD C:MET1 4.9 48.8 1.0 OG D:SER93 4.9 39.9 1.0

R.C.Bobde, A.Kumar, D.Vasudevan. Plant-Specific Hdt Family Histone Deacetylases Are Nucleoplasmins. Plant Cell V. 34 4760 2022.
ISSN: ESSN 1532-298X
PubMed: 36069647
DOI: 10.1093/PLCELL/KOAC275