Sodium in PDB 8ff6: Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum

Protein crystallography data

The structure of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum, PDB code: 8ff6 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) 49.36 / 2.49
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.558, 79.984, 80.147, 104.33, 111.17, 101.78
R / Rfree (%) 18.8 / 26.2

Other elements in 8ff6:

The structure of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum 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 (pdb code 8ff6). 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, PDB code: 8ff6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 8ff6

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Sodium binding site 1 out of 6 in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:38.2
occ:1.00
 O A:VAL185 2.5 36.8 1.0
O A:THR164 2.5 32.7 1.0
O A:ASN182 2.5 39.0 1.0
OG1 A:THR164 2.6 32.3 1.0
OD1 A:ASN182 2.7 43.8 1.0
OG1 A:THR180 2.9 37.7 1.0
CG A:ASN182 3.2 46.3 1.0
OD1 A:ASP187 3.4 36.2 1.0
ND2 A:ASN182 3.5 41.8 1.0
C A:THR164 3.5 32.9 1.0
C A:ASN182 3.5 43.7 1.0
C A:VAL185 3.7 37.1 1.0
CB A:THR164 3.7 32.2 1.0
CB A:THR180 3.9 36.5 1.0
CA A:THR164 3.9 32.1 1.0
CG2 A:THR180 4.2 31.8 1.0
CB A:ASN182 4.2 37.2 1.0
N A:VAL185 4.2 34.2 1.0
CG2 A:THR164 4.3 28.9 1.0
CG A:ASP187 4.3 39.8 1.0
CA A:ASN182 4.3 39.2 1.0
CA A:VAL185 4.4 34.8 1.0
CA A:PRO183 4.4 36.2 1.0
N A:PRO183 4.4 40.9 1.0
CB A:VAL185 4.4 38.5 1.0
N A:ASP187 4.6 32.0 1.0
N A:ASN182 4.6 40.5 1.0
CB A:SER189 4.6 36.1 1.0
N A:LEU165 4.7 32.5 1.0
N A:PHE186 4.8 34.8 1.0
OD2 A:ASP187 4.8 48.2 1.0
C A:PRO183 4.8 38.8 1.0
O A:ASP187 4.9 34.9 1.0

Sodium binding site 2 out of 6 in 8ff6

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:35.6
occ:1.00
 O B:THR164 2.1 37.6 1.0
OD1 B:ASN182 2.3 52.7 1.0
O B:VAL185 2.4 39.3 1.0
OG1 B:THR164 2.5 33.9 1.0
O B:ASN182 2.7 43.2 1.0
OG1 B:THR180 3.0 46.8 1.0
C B:THR164 3.1 38.6 1.0
CG B:ASN182 3.3 55.9 1.0
CB B:THR164 3.4 32.5 1.0
OD1 B:ASP187 3.5 42.1 1.0
C B:VAL185 3.6 41.7 1.0
C B:ASN182 3.6 42.6 1.0
CA B:THR164 3.6 34.1 1.0
CB B:THR180 3.9 47.2 1.0
CG2 B:THR164 4.0 33.7 1.0
CG2 B:THR180 4.0 37.6 1.0
ND2 B:ASN182 4.1 52.8 1.0
N B:VAL185 4.2 41.9 1.0
CG B:ASP187 4.3 41.6 1.0
N B:LEU165 4.3 37.5 1.0
CA B:VAL185 4.3 39.3 1.0
CB B:ASN182 4.3 44.1 1.0
CA B:PRO183 4.3 45.6 1.0
N B:PRO183 4.4 46.8 1.0
CA B:ASN182 4.4 42.1 1.0
CB B:VAL185 4.5 39.8 1.0
N B:ASP187 4.5 36.0 1.0
OD2 B:ASP187 4.6 39.9 1.0
N B:PHE186 4.6 42.4 1.0
C B:PRO183 4.7 43.0 1.0
N B:ASN182 4.7 47.0 1.0
CB B:SER189 4.7 39.0 1.0
CD2 B:LEU165 4.7 31.2 1.0
CA B:LEU165 4.8 38.8 1.0
CA B:PHE186 4.8 36.2 1.0
N B:LEU184 4.9 38.3 1.0
O B:ASP187 5.0 42.9 1.0

Sodium binding site 3 out of 6 in 8ff6

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:38.2
occ:1.00
 O C:THR164 2.3 43.7 1.0
OG1 C:THR164 2.4 42.1 1.0
O C:VAL185 2.5 39.9 1.0
OD1 C:ASN182 2.7 56.5 1.0
O C:ASN182 2.8 48.1 1.0
OG1 C:THR180 2.9 42.8 1.0
OD1 C:ASP187 3.1 42.5 1.0
C C:THR164 3.3 47.0 1.0
CB C:THR164 3.5 43.7 1.0
CG C:ASN182 3.6 57.6 1.0
CA C:THR164 3.7 47.7 1.0
CB C:THR180 3.7 51.6 1.0
C C:VAL185 3.7 38.4 1.0
CG2 C:THR180 3.8 47.8 1.0
C C:ASN182 3.8 50.4 1.0
CG C:ASP187 4.0 50.6 1.0
CG2 C:THR164 4.1 38.4 1.0
ND2 C:ASN182 4.3 53.2 1.0
N C:VAL185 4.4 38.6 1.0
N C:ASP187 4.4 43.2 1.0
CA C:VAL185 4.4 40.6 1.0
OD2 C:ASP187 4.5 52.6 1.0
CA C:PRO183 4.5 50.0 1.0
N C:LEU165 4.5 43.8 1.0
CB C:VAL185 4.6 47.6 1.0
N C:PRO183 4.6 51.0 1.0
CB C:ASN182 4.6 50.0 1.0
CB C:SER189 4.6 39.8 1.0
CA C:ASN182 4.7 47.1 1.0
N C:PHE186 4.7 42.7 1.0
CA C:PHE186 4.8 40.6 1.0
C C:PRO183 4.8 51.3 1.0
CG1 C:VAL185 4.9 40.0 1.0
N C:ASN182 4.9 50.6 1.0
O C:ASP187 5.0 39.3 1.0
CD2 C:LEU165 5.0 32.8 1.0

Sodium binding site 4 out of 6 in 8ff6

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:41.8
occ:1.00
 O D:THR164 2.2 46.5 1.0
O D:VAL185 2.4 47.6 1.0
OG1 D:THR164 2.5 43.5 1.0
OD1 D:ASN182 2.7 54.0 1.0
O D:ASN182 2.7 49.7 1.0
OG1 D:THR180 3.0 50.3 1.0
C D:THR164 3.3 46.5 1.0
C D:VAL185 3.5 50.7 1.0
C D:ASN182 3.6 49.9 1.0
CB D:THR164 3.6 45.3 1.0
OD1 D:ASP187 3.6 51.7 1.0
CG D:ASN182 3.7 59.4 1.0
CA D:THR164 3.8 47.3 1.0
CB D:THR180 4.0 52.6 1.0
CG2 D:THR180 4.1 49.4 1.0
CA D:PRO183 4.1 51.5 1.0
N D:VAL185 4.2 45.9 1.0
CG2 D:THR164 4.2 44.3 1.0
N D:PRO183 4.3 48.9 1.0
CA D:VAL185 4.3 51.1 1.0
CG D:ASP187 4.3 53.2 1.0
N D:LEU165 4.4 46.9 1.0
CB D:VAL185 4.4 43.7 1.0
C D:PRO183 4.5 47.3 1.0
ND2 D:ASN182 4.5 60.7 1.0
CA D:ASN182 4.5 50.9 1.0
O D:HOH452 4.5 44.7 1.0
CB D:ASN182 4.5 47.2 1.0
N D:PHE186 4.6 49.6 1.0
N D:ASP187 4.6 46.8 1.0
OD2 D:ASP187 4.7 49.3 1.0
N D:ASN182 4.7 49.3 1.0
CA D:LEU165 4.8 46.2 1.0
CA D:PHE186 4.8 46.6 1.0
CB D:SER189 4.8 51.9 1.0
CG1 D:VAL185 4.8 42.0 1.0
N D:LEU184 4.9 50.1 1.0
O D:PRO183 4.9 43.3 1.0

Sodium binding site 5 out of 6 in 8ff6

Go back to Sodium Binding Sites List in 8ff6
Sodium binding site 5 out of 6 in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:37.4
occ:1.00
 O E:THR164 2.2 38.1 1.0
OG1 E:THR164 2.4 40.2 1.0
O E:VAL185 2.5 43.3 1.0
OD1 E:ASN182 2.6 52.6 1.0
OG1 E:THR180 2.8 46.5 1.0
O E:ASN182 2.9 45.5 1.0
C E:THR164 3.2 43.2 1.0
CB E:THR164 3.5 40.9 1.0
CA E:THR164 3.6 41.6 1.0
C E:ASN182 3.6 48.3 1.0
CG E:ASN182 3.6 60.1 1.0
CB E:THR180 3.7 45.4 1.0
C E:VAL185 3.7 43.7 1.0
OD1 E:ASP187 3.7 41.5 1.0
CG2 E:THR180 3.9 39.9 1.0
CA E:PRO183 4.1 46.9 1.0
CG2 E:THR164 4.1 35.4 1.0
N E:VAL185 4.2 45.0 1.0
N E:PRO183 4.3 49.7 1.0
ND2 E:ASN182 4.4 50.9 1.0
CA E:VAL185 4.4 47.9 1.0
N E:LEU165 4.4 44.4 1.0
CA E:ASN182 4.5 45.5 1.0
C E:PRO183 4.6 44.8 1.0
CG E:ASP187 4.6 47.5 1.0
CB E:VAL185 4.6 46.1 1.0
CB E:ASN182 4.6 41.4 1.0
CD2 E:LEU165 4.7 37.1 1.0
N E:ASN182 4.7 50.5 1.0
N E:ASP187 4.7 35.1 1.0
CB E:SER189 4.8 38.4 1.0
N E:PHE186 4.8 40.6 1.0
O E:HOH426 4.8 43.9 1.0
N E:LEU184 4.8 44.6 1.0
CA E:LEU165 4.9 47.9 1.0
CA E:PHE186 5.0 41.3 1.0
OD2 E:ASP187 5.0 50.2 1.0

Sodium binding site 6 out of 6 in 8ff6

Go back to Sodium Binding Sites List in 8ff6
Sodium binding site 6 out of 6 in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na302

b:47.3
occ:1.00
 O F:THR164 2.1 53.8 1.0
OG1 F:THR164 2.2 51.2 1.0
OD1 F:ASN182 2.3 65.9 1.0
O F:VAL185 2.7 54.3 1.0
OG1 F:THR180 2.8 50.5 1.0
O F:ASN182 2.9 53.6 1.0
C F:THR164 3.0 53.6 1.0
CB F:THR164 3.2 56.8 1.0
CA F:THR164 3.3 55.6 1.0
OD1 F:ASP187 3.3 55.0 1.0
CG F:ASN182 3.5 65.9 1.0
CG2 F:THR164 3.7 51.0 1.0
CB F:THR180 3.7 58.1 1.0
C F:ASN182 3.8 55.6 1.0
CG2 F:THR180 3.9 49.6 1.0
C F:VAL185 3.9 50.9 1.0
O F:HOH405 4.1 52.4 1.0
N F:LEU165 4.2 52.9 1.0
ND2 F:ASN182 4.3 63.5 1.0
CG F:ASP187 4.4 54.1 1.0
N F:VAL185 4.5 47.8 1.0
CB F:ASN182 4.5 60.0 1.0
CA F:PRO183 4.5 54.7 1.0
N F:PRO183 4.5 56.7 1.0
CA F:ASN182 4.6 56.8 1.0
N F:ASP187 4.6 50.8 1.0
CA F:VAL185 4.7 48.0 1.0
CB F:SER189 4.7 56.1 1.0
N F:THR164 4.8 54.6 1.0
N F:ASN182 4.8 60.9 1.0
CA F:LEU165 4.8 56.7 1.0
C F:PRO183 4.8 52.8 1.0
OD2 F:ASP187 4.8 54.2 1.0
CB F:VAL185 4.9 50.1 1.0
N F:PHE186 4.9 46.3 1.0
O F:ASP187 5.0 50.8 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 18:54:59 2023

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