Sodium in PDB 8djt: Cytosolic Ascorbate Peroxidase From Sorghum Bicolor - Four Ascorbates Complex

Enzymatic activity of Cytosolic Ascorbate Peroxidase From Sorghum Bicolor - Four Ascorbates Complex

All present enzymatic activity of Cytosolic Ascorbate Peroxidase From Sorghum Bicolor - Four Ascorbates Complex:
1.11.1.11;

Protein crystallography data

The structure of Cytosolic Ascorbate Peroxidase From Sorghum Bicolor - Four Ascorbates Complex, PDB code: 8djt 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) 31.55 / 1.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.296, 75.097, 82.997, 90, 90, 90
R / Rfree (%) 13.8 / 15.1

Other elements in 8djt:

The structure of Cytosolic Ascorbate Peroxidase From Sorghum Bicolor - Four Ascorbates Complex 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 - Four Ascorbates Complex (pdb code 8djt). 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 - Four Ascorbates Complex, PDB code: 8djt:

Sodium binding site 1 out of 1 in 8djt

Go back to Sodium Binding Sites List in 8djt
Sodium binding site 1 out of 1 in the Cytosolic Ascorbate Peroxidase From Sorghum Bicolor - Four Ascorbates Complex


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 - Four Ascorbates Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:7.4
occ:1.00
 HG1 A:THR180 1.9 9.2 1.0
O A:THR164 2.2 6.4 1.0
O A:ASN182 2.3 7.0 1.0
O A:VAL185 2.4 6.8 1.0
OG1 A:THR164 2.6 11.8 1.0
OD1 A:ASN182 2.6 21.8 1.0
HG1 A:THR164 2.7 14.2 1.0
OG1 A:THR180 2.7 7.7 1.0
C A:THR164 3.3 5.9 1.0
C A:ASN182 3.3 7.8 1.0
CG A:ASN182 3.3 17.5 1.0
H A:VAL185 3.4 7.2 1.0
HG21 A:THR180 3.4 9.8 1.0
HA A:PRO183 3.5 8.3 1.0
HA A:THR164 3.5 7.5 1.0
HB A:THR180 3.5 8.5 1.0
HB A:VAL185 3.6 8.9 1.0
C A:VAL185 3.6 6.0 1.0
CB A:THR180 3.6 7.1 1.0
CB A:THR164 3.7 8.3 1.0
CA A:THR164 3.7 6.3 1.0
H A:ASN182 3.8 9.7 1.0
HG23 A:THR164 3.9 10.8 1.0
CG2 A:THR180 4.0 8.2 1.0
HD23 A:LEU165 4.0 7.9 1.0
OD1 A:ASP187 4.0 11.2 1.0
N A:VAL185 4.0 6.0 1.0
HD22 A:ASN182 4.1 26.6 1.0
ND2 A:ASN182 4.1 22.1 1.0
N A:PRO183 4.1 6.9 1.0
CA A:PRO183 4.1 6.9 1.0
CA A:ASN182 4.2 8.6 1.0
CA A:VAL185 4.2 6.6 1.0
CB A:ASN182 4.2 10.8 1.0
HA A:LEU165 4.2 6.4 1.0
HB2 A:SER189 4.3 13.1 1.0
CB A:VAL185 4.3 7.4 1.0
H A:ASP187 4.3 8.2 1.0
CG2 A:THR164 4.3 9.0 1.0
HG23 A:THR180 4.3 9.8 1.0
HB2 A:ASN182 4.4 13.0 1.0
HG12 A:VAL185 4.4 13.3 1.0
N A:LEU165 4.4 4.9 1.0
N A:ASN182 4.4 8.1 1.0
HB A:THR164 4.4 10.0 1.0
HA A:PHE186 4.5 7.0 1.0
C A:PRO183 4.5 5.8 1.0
O A:HOH536 4.7 6.7 1.0
CG A:ASP187 4.7 10.5 1.0
N A:PHE186 4.7 5.7 1.0
HG22 A:THR180 4.8 9.8 1.0
HD21 A:ASN182 4.8 26.6 1.0
HG21 A:THR164 4.8 10.8 1.0
N A:LEU184 4.8 6.1 1.0
CA A:LEU165 4.9 5.3 1.0
CG1 A:VAL185 4.9 11.1 1.0
O A:PRO183 4.9 6.2 1.0
H A:LEU184 4.9 7.3 1.0
N A:ASP187 4.9 6.9 1.0
CD2 A:LEU165 5.0 6.5 1.0
OD2 A:ASP187 5.0 17.4 1.0
CA A:THR180 5.0 7.2 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: Fri Apr 7 18:45:02 2023

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