Sodium in PDB 8djr: Cytosolic Ascorbate Peroxidase From Sorghum Bicolor

All present enzymatic activity of Cytosolic Ascorbate Peroxidase From Sorghum Bicolor:
1.11.1.11;

The structure of Cytosolic Ascorbate Peroxidase From Sorghum Bicolor, PDB code: 8djr was solved by B.Zhang, C.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.69 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.207, 75.068, 83.381, 90, 90, 90
R / Rfree (%)	12.5 / 14.5

The structure of Cytosolic Ascorbate Peroxidase From Sorghum Bicolor also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Sodium atom in the Cytosolic Ascorbate Peroxidase From Sorghum Bicolor (pdb code 8djr). 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 Cytosolic Ascorbate Peroxidase From Sorghum Bicolor, PDB code: 8djr:

Sodium binding site 1 out of 1 in the Cytosolic Ascorbate Peroxidase From Sorghum Bicolor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cytosolic Ascorbate Peroxidase From Sorghum Bicolor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:13.7 occ:1.00 HG1 A:THR180 2.3 5.2 1.0 O A:VAL185 2.7 5.0 1.0 O A:THR164 2.7 4.1 1.0 O A:ASN182 2.9 3.9 1.0 OD1 A:ASN182 2.9 4.8 1.0 OD1 A:ASP187 3.0 4.6 1.0 OG1 A:THR164 3.0 5.4 1.0 OG1 A:THR180 3.1 4.4 1.0 HG21 A:THR180 3.2 5.1 1.0 HB2 A:SER189 3.3 8.0 1.0 HG1 A:THR164 3.4 6.5 1.0 HB A:THR180 3.5 4.7 1.0 CG A:ASN182 3.5 5.8 1.0 HG23 A:THR164 3.6 4.5 1.0 C A:THR164 3.7 3.5 1.0 CB A:THR180 3.7 4.0 1.0 HA A:PRO183 3.7 4.2 1.0 C A:ASN182 3.8 4.2 1.0 HB A:VAL185 3.8 4.7 1.0 HA A:THR164 3.8 3.7 1.0 CG A:ASP187 3.8 5.1 1.0 HD21 A:ASN182 3.8 7.1 1.0 H A:VAL185 3.8 3.8 1.0 CG2 A:THR180 3.9 4.3 1.0 C A:VAL185 3.9 4.2 1.0 H A:ASP187 3.9 4.8 1.0 CB A:THR164 4.0 3.6 1.0 ND2 A:ASN182 4.0 6.0 1.0 CA A:THR164 4.0 3.1 1.0 H A:ASN182 4.1 5.3 1.0 OD2 A:ASP187 4.1 7.5 1.0 CB A:SER189 4.2 6.7 1.0 HG A:SER189 4.2 11.5 1.0 CG2 A:THR164 4.3 3.8 1.0 HD23 A:LEU165 4.3 6.6 1.0 HG23 A:THR180 4.4 5.1 1.0 H A:SER189 4.4 4.3 1.0 CA A:PRO183 4.5 3.5 1.0 CB A:ASN182 4.5 4.7 1.0 HG12 A:VAL185 4.5 9.6 1.0 N A:VAL185 4.5 3.2 1.0 OG A:SER189 4.5 9.6 1.0 N A:PRO183 4.5 3.5 1.0 CB A:VAL185 4.5 4.0 1.0 N A:ASP187 4.5 4.1 1.0 CA A:VAL185 4.5 4.2 1.0 CA A:ASN182 4.5 4.2 1.0 HG22 A:THR180 4.6 5.1 1.0 HA A:PHE186 4.6 2.8 1.0 HB3 A:SER189 4.6 8.0 1.0 HD22 A:ASN182 4.6 7.1 1.0 HA A:LEU165 4.6 4.5 1.0 HB2 A:ASN182 4.7 5.5 1.0 N A:ASN182 4.7 4.5 1.0 HG21 A:THR164 4.8 4.5 1.0 N A:LEU165 4.8 2.6 1.0 HB A:THR164 4.8 4.3 1.0 H A:TYR190 4.9 5.2 1.0 N A:PHE186 4.9 2.8 1.0 CB A:ASP187 5.0 4.5 1.0 C A:PRO183 5.0 4.0 1.0 O A:ASP187 5.0 4.3 1.0 HG22 A:THR164 5.0 4.5 1.0

B.Zhang, J.A.Lewis, W.Vermerris, S.E.Sattler, C.Kang. A Sorghum Ascorbate Peroxidase with Four Binding Sites Has Activity Against Ascorbate and Phenylpropanoids. Plant Physiol. 2022.
ISSN: ESSN 1532-2548
PubMed: 36575825
DOI: 10.1093/PLPHYS/KIAC604