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Sodium in PDB 1iyn: Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability

Enzymatic activity of Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability

All present enzymatic activity of Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability:
1.11.1.11;

Protein crystallography data

The structure of Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability, PDB code: 1iyn was solved by K.Wada, T.Tada, Y.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.99 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.188, 76.790, 98.776, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.2

Other elements in 1iyn:

The structure of Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability also contains other interesting chemical elements:

Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability (pdb code 1iyn). 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 Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability, PDB code: 1iyn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1iyn

Go back to Sodium Binding Sites List in 1iyn
Sodium binding site 1 out of 2 in the Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability


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 Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na297

b:8.6
occ:1.00
 O A:THR164 2.4 7.5 1.0
O A:LYS201 2.5 9.3 1.0
O A:GLN198 2.5 8.7 1.0
OG1 A:THR164 2.6 6.2 1.0
OG1 A:THR196 2.8 7.1 1.0
O A:HOH312 2.9 22.8 1.0
C A:THR164 3.3 7.5 1.0
C A:GLN198 3.5 8.6 1.0
C A:LYS201 3.6 8.7 1.0
CB A:THR196 3.6 8.6 1.0
CB A:THR164 3.7 5.8 1.0
CA A:THR164 3.8 3.8 1.0
CA A:TRP199 3.9 8.7 1.0
OD2 A:ASP203 4.0 13.7 1.0
CG2 A:THR196 4.0 6.6 1.0
N A:LYS201 4.0 9.6 1.0
N A:TRP199 4.1 8.0 1.0
CG2 A:THR164 4.2 10.4 1.0
CA A:LYS201 4.2 8.8 1.0
CB A:LYS201 4.3 10.9 1.0
C A:TRP199 4.4 9.8 1.0
N A:LEU165 4.5 7.5 1.0
CA A:GLN198 4.5 12.2 1.0
N A:LEU200 4.7 7.5 1.0
CB A:GLN198 4.7 13.4 1.0
CG A:ASP203 4.7 16.0 1.0
N A:PHE202 4.7 8.0 1.0
O A:HOH328 4.7 13.7 1.0
N A:GLN198 4.8 9.9 1.0
N A:ASP203 4.8 9.4 1.0
CA A:PHE202 4.9 8.2 1.0
CA A:LEU165 5.0 9.4 1.0
O A:TRP199 5.0 9.1 1.0
OD1 A:ASP203 5.0 19.0 1.0
CD2 A:LEU165 5.0 9.3 1.0

Sodium binding site 2 out of 2 in 1iyn

Go back to Sodium Binding Sites List in 1iyn
Sodium binding site 2 out of 2 in the Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability


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 Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na298

b:9.4
occ:1.00
 O A:GLY51 2.4 6.6 1.0
O A:HOH306 2.4 13.8 1.0
OD1 A:ASN53 2.5 8.4 1.0
OD2 A:ASP35 2.5 8.2 1.0
OG A:SER55 2.6 12.1 1.0
CG A:ASN53 3.3 8.6 1.0
O A:ASP35 3.4 7.2 1.0
CG A:ASP35 3.4 10.2 1.0
C A:GLY51 3.6 10.2 1.0
CB A:SER55 3.6 6.7 1.0
N A:SER55 3.7 7.8 1.0
ND2 A:ASN53 3.8 7.8 1.0
N A:ASN53 3.8 6.9 1.0
OD1 A:ASP35 4.0 7.2 1.0
N A:GLY51 4.1 7.6 1.0
C A:ASP35 4.1 7.5 1.0
OG1 A:THR38 4.2 8.6 1.0
CA A:SER55 4.2 10.0 1.0
N A:LEU56 4.2 9.9 1.0
N A:GLY54 4.3 7.3 1.0
CA A:ASP35 4.3 8.8 1.0
OE2 A:GLU61 4.3 9.1 1.0
CA A:GLY51 4.4 7.3 1.0
CB A:ASP35 4.5 8.9 1.0
CB A:ASN53 4.5 6.6 1.0
OE1 A:GLU61 4.5 8.5 1.0
CA A:ASN53 4.5 8.8 1.0
C A:ASN53 4.5 9.1 1.0
O A:HOH317 4.6 12.7 1.0
N A:ALA52 4.6 7.0 1.0
C A:SER55 4.6 8.8 1.0
C A:GLY50 4.7 9.5 1.0
C A:GLY54 4.7 8.2 1.0
CA A:ALA52 4.8 7.9 1.0
CD A:PRO125 4.8 12.7 1.0
C A:ALA52 4.8 9.1 1.0
CD A:GLU61 4.8 9.6 1.0
CA A:GLY54 4.9 6.9 1.0

Reference:

K.Wada, T.Tada, Y.Nakamura, T.Ishikawa, Y.Yabuta, K.Yoshimura, S.Shigeoka, K.Nishimura. Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights Into Its Instability J.Biochem.(Tokyo) V. 134 239 2003.
ISSN: ISSN 0021-924X
PubMed: 12966073
DOI: 10.1093/JB/MVG136
Page generated: Sun Oct 6 18:53:49 2024

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