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Sodium in PDB 8djx: Cytosolic Ascorbate Peroxidase From Sorghum Bicolor - Compound II

Enzymatic activity of Cytosolic Ascorbate Peroxidase From Sorghum Bicolor - Compound II

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

Protein crystallography data

The structure of Cytosolic Ascorbate Peroxidase From Sorghum Bicolor - Compound II, PDB code: 8djx 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) 41.49 / 1.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.07, 74.742, 82.972, 90, 90, 90
R / Rfree (%) 14 / 15

Other elements in 8djx:

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

Iron (Fe) 1 atom

Sodium Binding Sites:

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

Sodium binding site 1 out of 1 in 8djx

Go back to Sodium Binding Sites List in 8djx
Sodium binding site 1 out of 1 in the Cytosolic Ascorbate Peroxidase From Sorghum Bicolor - Compound II


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 - Compound II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:25.0
occ:1.00
 HG1 A:THR180 2.3 9.8 1.0
O A:VAL185 2.7 8.4 1.0
O A:THR164 2.7 8.8 1.0
O A:ASN182 2.8 8.4 1.0
OD1 A:ASN182 2.9 8.9 1.0
OG1 A:THR180 3.1 8.2 1.0
OD1 A:ASP187 3.1 8.1 1.0
HG21 A:THR180 3.1 10.4 1.0
OG1 A:THR164 3.1 9.7 1.0
HB2 A:SER189 3.3 13.0 1.0
HB A:THR180 3.4 10.1 1.0
CG A:ASN182 3.5 10.0 1.0
HG1 A:THR164 3.5 11.7 1.0
CB A:THR180 3.6 8.4 1.0
HA A:PRO183 3.7 9.6 1.0
C A:THR164 3.7 7.0 1.0
C A:ASN182 3.7 8.9 1.0
HG23 A:THR164 3.7 9.8 1.0
HB A:VAL185 3.7 9.1 1.0
HD21 A:ASN182 3.8 11.2 1.0
CG2 A:THR180 3.8 8.7 1.0
H A:VAL185 3.8 7.9 1.0
CG A:ASP187 3.8 8.7 1.0
HA A:THR164 3.9 9.1 1.0
C A:VAL185 3.9 7.0 1.0
H A:ASP187 3.9 8.8 1.0
ND2 A:ASN182 3.9 9.4 1.0
CB A:THR164 4.0 8.7 1.0
H A:ASN182 4.1 10.5 1.0
CA A:THR164 4.1 7.6 1.0
OD2 A:ASP187 4.1 11.1 1.0
CB A:SER189 4.2 10.8 1.0
HG A:SER189 4.2 14.8 1.0
HD23 A:LEU165 4.3 10.3 1.0
HG23 A:THR180 4.3 10.4 1.0
CG2 A:THR164 4.4 8.1 1.0
CA A:PRO183 4.4 8.0 1.0
N A:PRO183 4.5 8.2 1.0
CB A:ASN182 4.5 9.7 1.0
CA A:ASN182 4.5 9.6 1.0
N A:VAL185 4.5 6.6 1.0
CB A:VAL185 4.5 7.6 1.0
HG12 A:VAL185 4.5 13.3 1.0
H A:SER189 4.5 9.6 1.0
HG22 A:THR180 4.5 10.4 1.0
N A:ASP187 4.5 7.3 1.0
CA A:VAL185 4.5 7.5 1.0
OG A:SER189 4.5 12.3 1.0
HA A:LEU165 4.6 8.8 1.0
HA A:PHE186 4.6 7.4 1.0
HB3 A:SER189 4.6 13.0 1.0
HD22 A:ASN182 4.6 11.2 1.0
HB2 A:ASN182 4.6 11.6 1.0
N A:ASN182 4.7 8.8 1.0
N A:LEU165 4.8 6.3 1.0
HG21 A:THR164 4.9 9.8 1.0
C A:PRO183 4.9 7.4 1.0
HB A:THR164 4.9 10.5 1.0
N A:PHE186 4.9 6.8 1.0
H A:TYR190 4.9 9.3 1.0
CB A:ASP187 5.0 8.4 1.0

Reference:

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
Page generated: Mon Aug 18 13:53:16 2025

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