Sodium in PDB 8ff7: Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex

Protein crystallography data

The structure of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex, PDB code: 8ff7 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) 49.23 / 2.19
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.267, 80.176, 80.166, 104.55, 101.97, 110.73
R / Rfree (%) 18.8 / 24.2

Other elements in 8ff7:

The structure of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex also contains other interesting chemical elements:

Iron (Fe) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex (pdb code 8ff7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex, PDB code: 8ff7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 8ff7

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Sodium binding site 1 out of 6 in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate 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 Mutant From Panicum Virgatum- Ascorbate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:24.5
occ:1.00
 O A:ASN182 2.4 26.1 1.0
O A:THR164 2.5 18.2 1.0
O A:VAL185 2.6 21.7 1.0
OG1 A:THR164 2.6 24.9 1.0
OG1 A:THR180 2.7 22.9 1.0
ND2 A:ASN182 3.3 31.0 1.0
CG A:ASN182 3.3 36.2 1.0
C A:ASN182 3.3 25.2 1.0
C A:THR164 3.5 19.1 1.0
OD1 A:ASN182 3.5 43.8 1.0
OD1 A:ASP187 3.6 27.8 1.0
CB A:THR164 3.6 25.5 1.0
CB A:THR180 3.7 27.5 1.0
C A:VAL185 3.7 26.9 1.0
CA A:THR164 3.8 21.7 1.0
CG2 A:THR180 4.0 22.2 1.0
CB A:ASN182 4.0 28.4 1.0
CA A:ASN182 4.1 27.8 1.0
CG2 A:THR164 4.1 18.0 1.0
N A:PRO183 4.2 27.3 1.0
N A:VAL185 4.2 23.1 1.0
CA A:PRO183 4.3 24.1 1.0
CG A:ASP187 4.3 28.5 1.0
CA A:VAL185 4.3 25.6 1.0
N A:ASN182 4.4 31.4 1.0
CB A:VAL185 4.4 27.9 1.0
N A:LEU165 4.6 18.8 1.0
OD2 A:ASP187 4.6 27.7 1.0
CB A:SER189 4.7 23.8 1.0
C A:PRO183 4.7 25.7 1.0
N A:ASP187 4.8 25.3 1.0
N A:PHE186 4.8 22.1 1.0
CG1 A:VAL185 4.9 30.7 1.0
CD2 A:LEU165 4.9 19.8 1.0

Sodium binding site 2 out of 6 in 8ff7

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Sodium binding site 2 out of 6 in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:26.4
occ:1.00
 O B:THR164 2.1 26.7 1.0
O B:VAL185 2.5 24.4 1.0
OG1 B:THR164 2.5 32.9 1.0
OD1 B:ASN182 2.5 40.9 1.0
O B:ASN182 2.6 29.2 1.0
OG1 B:THR180 2.6 33.0 1.0
C B:THR164 3.1 28.1 1.0
CB B:THR164 3.4 29.6 1.0
CA B:THR164 3.4 24.0 1.0
C B:ASN182 3.5 29.2 1.0
CB B:THR180 3.6 33.1 1.0
CG B:ASN182 3.6 44.9 1.0
OD1 B:ASP187 3.7 31.9 1.0
C B:VAL185 3.7 30.0 1.0
CG2 B:THR180 3.9 27.3 1.0
CG2 B:THR164 4.0 27.6 1.0
CA B:PRO183 4.1 29.1 1.0
N B:PRO183 4.1 31.2 1.0
N B:VAL185 4.2 27.5 1.0
N B:LEU165 4.3 25.3 1.0
CA B:VAL185 4.3 28.8 1.0
CA B:ASN182 4.3 33.6 1.0
ND2 B:ASN182 4.4 41.7 1.0
CB B:VAL185 4.5 27.1 1.0
CB B:ASN182 4.5 30.6 1.0
N B:ASN182 4.5 37.0 1.0
CG B:ASP187 4.5 35.8 1.0
C B:PRO183 4.6 26.5 1.0
O B:HOH479 4.7 28.1 1.0
N B:PHE186 4.7 24.1 1.0
CA B:LEU165 4.8 30.5 1.0
CD2 B:LEU165 4.8 25.8 1.0
N B:ASP187 4.8 28.1 1.0
CB B:SER189 4.9 29.0 1.0
N B:THR164 4.9 30.6 1.0
OD2 B:ASP187 4.9 41.3 1.0
N B:LEU184 4.9 21.5 1.0
CA B:THR180 4.9 33.0 1.0
CA B:PHE186 5.0 22.7 1.0

Sodium binding site 3 out of 6 in 8ff7

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Sodium binding site 3 out of 6 in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:32.1
occ:1.00
 O C:VAL185 2.4 26.9 1.0
OG1 C:THR164 2.5 31.4 1.0
O C:THR164 2.6 30.2 1.0
O C:ASN182 2.7 36.8 1.0
OG1 C:THR180 2.9 30.8 1.0
OD1 C:ASN182 3.0 44.9 1.0
CG C:ASN182 3.4 42.9 1.0
C C:THR164 3.5 28.1 1.0
OD1 C:ASP187 3.6 28.4 1.0
C C:ASN182 3.6 36.6 1.0
C C:VAL185 3.6 29.9 1.0
CB C:THR164 3.7 27.6 1.0
CB C:THR180 3.7 38.0 1.0
ND2 C:ASN182 3.8 45.3 1.0
CA C:THR164 3.9 28.9 1.0
CG2 C:THR180 3.9 33.6 1.0
CG C:ASP187 4.2 34.0 1.0
CG2 C:THR164 4.2 27.6 1.0
N C:VAL185 4.3 30.3 1.0
CA C:VAL185 4.3 31.5 1.0
CB C:ASN182 4.3 34.0 1.0
CB C:VAL185 4.3 30.8 1.0
CA C:ASN182 4.4 35.0 1.0
N C:PRO183 4.5 32.8 1.0
N C:ASP187 4.5 30.4 1.0
CA C:PRO183 4.5 33.9 1.0
OD2 C:ASP187 4.5 38.4 1.0
CB C:SER189 4.6 32.0 1.0
N C:ASN182 4.6 37.0 1.0
N C:LEU165 4.7 26.1 1.0
N C:PHE186 4.7 26.1 1.0
C C:PRO183 4.9 34.0 1.0
CG1 C:VAL185 4.9 26.4 1.0
CA C:PHE186 4.9 26.7 1.0
OG C:SER189 4.9 33.2 1.0
O C:HOH462 5.0 31.6 1.0

Sodium binding site 4 out of 6 in 8ff7

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Sodium binding site 4 out of 6 in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:25.8
occ:1.00
 O D:THR164 2.2 19.5 1.0
O D:ASN182 2.4 30.7 1.0
O D:VAL185 2.4 25.4 1.0
OG1 D:THR164 2.6 26.6 1.0
OG1 D:THR180 2.7 26.2 1.0
OD1 D:ASN182 3.1 45.6 1.0
C D:THR164 3.3 24.1 1.0
C D:ASN182 3.4 33.1 1.0
C D:VAL185 3.6 28.1 1.0
CB D:THR164 3.7 23.9 1.0
CB D:THR180 3.7 31.7 1.0
CA D:THR164 3.8 22.0 1.0
N D:VAL185 4.0 24.6 1.0
CG2 D:THR180 4.1 26.3 1.0
OD1 D:ASP187 4.1 26.3 1.0
CG D:ASN182 4.1 48.2 1.0
CA D:VAL185 4.2 25.1 1.0
CA D:PRO183 4.2 32.6 1.0
N D:PRO183 4.2 28.9 1.0
CB D:VAL185 4.3 28.6 1.0
CA D:ASN182 4.3 36.1 1.0
CG2 D:THR164 4.4 24.1 1.0
N D:LEU165 4.4 20.8 1.0
N D:ASN182 4.4 36.8 1.0
C D:PRO183 4.5 26.8 1.0
CB D:ASN182 4.5 30.2 1.0
CG D:ASP187 4.7 29.5 1.0
N D:PHE186 4.7 26.0 1.0
N D:LEU184 4.8 25.6 1.0
O D:HOH433 4.8 30.1 1.0
CA D:LEU165 4.9 20.9 1.0
N D:ASP187 4.9 25.8 1.0
O D:PRO183 4.9 26.2 1.0
OD2 D:ASP187 5.0 35.6 1.0
CG1 D:VAL185 5.0 27.4 1.0
CB D:SER189 5.0 30.3 1.0

Sodium binding site 5 out of 6 in 8ff7

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Sodium binding site 5 out of 6 in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:31.0
occ:1.00
 OD1 E:ASN182 2.3 37.4 1.0
O E:THR164 2.5 24.6 1.0
O E:ASN182 2.5 29.8 1.0
OG1 E:THR164 2.5 26.1 1.0
O E:VAL185 2.6 27.1 1.0
OG1 E:THR180 2.7 27.6 1.0
CG E:ASN182 3.2 39.7 1.0
C E:ASN182 3.4 29.9 1.0
C E:THR164 3.5 27.2 1.0
CB E:THR180 3.5 33.6 1.0
OD1 E:ASP187 3.6 31.7 1.0
CB E:THR164 3.6 21.4 1.0
C E:VAL185 3.7 28.8 1.0
ND2 E:ASN182 3.8 43.2 1.0
CA E:THR164 3.8 26.1 1.0
CG2 E:THR180 3.8 25.3 1.0
CA E:ASN182 4.2 32.3 1.0
CB E:ASN182 4.2 33.5 1.0
CG2 E:THR164 4.3 23.4 1.0
N E:VAL185 4.3 27.1 1.0
N E:PRO183 4.3 31.9 1.0
N E:ASN182 4.3 30.7 1.0
CG E:ASP187 4.4 31.9 1.0
CA E:PRO183 4.4 30.5 1.0
CA E:VAL185 4.4 26.8 1.0
CB E:VAL185 4.5 28.7 1.0
CB E:SER189 4.6 26.4 1.0
N E:LEU165 4.6 23.8 1.0
OD2 E:ASP187 4.7 37.7 1.0
O E:HOH479 4.7 31.7 1.0
N E:ASP187 4.7 28.3 1.0
N E:PHE186 4.8 25.0 1.0
C E:PRO183 4.8 32.0 1.0
CA E:THR180 4.9 26.7 1.0
N E:LEU184 5.0 30.8 1.0

Sodium binding site 6 out of 6 in 8ff7

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Sodium binding site 6 out of 6 in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na303

b:36.4
occ:1.00
 O F:THR164 2.3 32.8 1.0
O F:ASN182 2.3 33.0 1.0
O F:VAL185 2.5 29.8 1.0
OD1 F:ASN182 2.5 41.5 1.0
OG1 F:THR164 2.6 32.6 1.0
OG1 F:THR180 2.7 34.5 1.0
C F:ASN182 3.2 38.6 1.0
C F:THR164 3.4 31.4 1.0
CG F:ASN182 3.4 41.2 1.0
C F:VAL185 3.6 31.1 1.0
CB F:THR180 3.7 38.2 1.0
CB F:THR164 3.7 32.8 1.0
OD1 F:ASP187 3.7 33.4 1.0
CA F:THR164 3.8 35.2 1.0
CA F:ASN182 4.0 37.4 1.0
N F:PRO183 4.1 37.2 1.0
CB F:ASN182 4.1 38.7 1.0
CG2 F:THR180 4.1 37.2 1.0
N F:VAL185 4.1 31.3 1.0
CA F:PRO183 4.2 31.1 1.0
N F:ASN182 4.2 40.2 1.0
CA F:VAL185 4.3 31.9 1.0
ND2 F:ASN182 4.3 41.7 1.0
CG2 F:THR164 4.3 28.1 1.0
CB F:VAL185 4.4 32.8 1.0
CG F:ASP187 4.4 35.7 1.0
N F:LEU165 4.5 28.3 1.0
C F:PRO183 4.5 28.1 1.0
N F:ASP187 4.7 32.2 1.0
N F:PHE186 4.7 30.1 1.0
O F:HOH462 4.8 34.7 1.0
OD2 F:ASP187 4.8 37.4 1.0
CB F:SER189 4.9 35.0 1.0
N F:LEU184 4.9 32.0 1.0
CD2 F:LEU165 4.9 27.4 1.0
CA F:PHE186 5.0 29.6 1.0
CA F:LEU165 5.0 33.5 1.0

Reference:

B.Zhang, J.A.Lewis, F.Kovacs, S.E.Sattler, G.Sarath, C.Kang. Activity of Cytosolic Ascorbate Peroxidase (Apx) From Panicum Virgatum Against Ascorbate and Phenylpropanoids. Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
PubMed: 36675291
DOI: 10.3390/IJMS24021778
Page generated: Fri Apr 7 18:55:01 2023

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