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

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

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

Sodium

(Na)

6 atoms

The binding sites of Iron 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 Iron atom.
In total 6 binding sites of Iron where determined in the Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum- Ascorbate Complex, PDB code: 8ff7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:27.0 occ:1.00 FE A:HEM302 0.0 27.0 1.0 NB A:HEM302 2.0 26.7 1.0 ND A:HEM302 2.0 19.9 1.0 NE2 A:HIS163 2.0 26.5 1.0 NC A:HEM302 2.1 23.6 1.0 NA A:HEM302 2.1 25.2 1.0 O A:HOH483 2.5 28.4 1.0 CD2 A:HIS163 2.9 24.3 1.0 C4B A:HEM302 3.0 28.1 1.0 C1D A:HEM302 3.0 20.4 1.0 C1B A:HEM302 3.0 28.4 1.0 C4A A:HEM302 3.0 22.6 1.0 C4C A:HEM302 3.1 23.4 1.0 C4D A:HEM302 3.1 25.7 1.0 C1C A:HEM302 3.1 24.3 1.0 C1A A:HEM302 3.1 26.1 1.0 CE1 A:HIS163 3.2 25.3 1.0 CHD A:HEM302 3.4 22.8 1.0 CHB A:HEM302 3.4 26.7 1.0 CHC A:HEM302 3.4 25.5 1.0 CHA A:HEM302 3.5 24.5 1.0 CG A:HIS163 4.1 28.0 1.0 ND1 A:HIS163 4.2 24.5 1.0 C3B A:HEM302 4.2 26.2 1.0 C2D A:HEM302 4.2 21.1 1.0 C2B A:HEM302 4.2 29.0 1.0 NE1 A:TRP41 4.3 24.7 1.0 C3D A:HEM302 4.3 22.7 1.0 C3A A:HEM302 4.3 25.9 1.0 C2A A:HEM302 4.3 26.8 1.0 C3C A:HEM302 4.3 24.0 1.0 C2C A:HEM302 4.3 23.8 1.0 HHD A:HEM302 4.4 27.3 1.0 HHB A:HEM302 4.4 32.0 1.0 HHC A:HEM302 4.4 30.5 1.0 HHA A:HEM302 4.4 29.3 1.0 O A:HOH530 4.4 27.1 1.0 CD1 A:TRP41 4.5 25.2 1.0 O A:HOH509 4.5 28.8 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:31.9 occ:1.00 FE B:HEM302 0.0 31.9 1.0 NB B:HEM302 2.0 39.6 1.0 NC B:HEM302 2.0 32.2 1.0 NE2 B:HIS163 2.1 32.3 1.0 NA B:HEM302 2.1 41.5 1.0 ND B:HEM302 2.1 34.7 1.0 O B:HOH454 2.7 38.0 1.0 C4B B:HEM302 3.0 36.6 1.0 C1B B:HEM302 3.0 42.2 1.0 C1C B:HEM302 3.0 34.5 1.0 C4C B:HEM302 3.0 30.3 1.0 CD2 B:HIS163 3.1 30.6 1.0 CE1 B:HIS163 3.1 35.4 1.0 C1D B:HEM302 3.1 32.2 1.0 C4A B:HEM302 3.1 44.2 1.0 C4D B:HEM302 3.1 32.7 1.0 C1A B:HEM302 3.1 39.0 1.0 CHC B:HEM302 3.4 33.2 1.0 CHB B:HEM302 3.4 41.7 1.0 CHD B:HEM302 3.4 28.8 1.0 CHA B:HEM302 3.5 36.1 1.0 O B:HOH407 4.0 38.2 1.0 C3B B:HEM302 4.1 42.0 1.0 C2B B:HEM302 4.2 46.0 1.0 ND1 B:HIS163 4.2 29.3 1.0 CG B:HIS163 4.2 31.4 1.0 NE1 B:TRP41 4.2 33.5 1.0 C2C B:HEM302 4.2 32.4 1.0 C3C B:HEM302 4.3 34.2 1.0 C2D B:HEM302 4.3 33.2 1.0 C3D B:HEM302 4.3 32.6 1.0 C3A B:HEM302 4.3 42.1 1.0 C2A B:HEM302 4.3 39.7 1.0 HHC B:HEM302 4.3 39.8 1.0 HHB B:HEM302 4.4 50.0 1.0 HHD B:HEM302 4.4 34.5 1.0 HHA B:HEM302 4.5 43.2 1.0 O B:HOH443 4.6 38.8 1.0 CD1 B:TRP41 4.7 30.0 1.0 CH2 B:TRP179 4.9 37.1 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:32.6 occ:1.00 FE C:HEM302 0.0 32.6 1.0 NB C:HEM302 2.0 36.8 1.0 NA C:HEM302 2.0 40.4 1.0 NC C:HEM302 2.1 31.9 1.0 ND C:HEM302 2.1 35.6 1.0 NE2 C:HIS163 2.1 36.4 1.0 O C:HOH494 2.5 36.6 1.0 CD2 C:HIS163 2.9 33.1 1.0 C1B C:HEM302 2.9 38.1 1.0 C4A C:HEM302 3.0 35.4 1.0 C4B C:HEM302 3.0 35.7 1.0 C1A C:HEM302 3.1 35.4 1.0 C4C C:HEM302 3.1 29.7 1.0 C1C C:HEM302 3.1 33.5 1.0 C1D C:HEM302 3.1 31.8 1.0 C4D C:HEM302 3.1 36.8 1.0 CE1 C:HIS163 3.3 32.1 1.0 CHB C:HEM302 3.3 38.1 1.0 CHC C:HEM302 3.4 33.2 1.0 CHD C:HEM302 3.5 28.6 1.0 CHA C:HEM302 3.5 37.5 1.0 O C:HOH438 3.9 32.9 1.0 CG C:HIS163 4.1 33.0 1.0 C2B C:HEM302 4.1 42.2 1.0 C3B C:HEM302 4.2 40.5 1.0 C3A C:HEM302 4.2 42.4 1.0 C2A C:HEM302 4.2 42.9 1.0 ND1 C:HIS163 4.3 31.9 1.0 HHB C:HEM302 4.3 45.6 1.0 C2D C:HEM302 4.3 31.7 1.0 C3C C:HEM302 4.3 30.3 1.0 C3D C:HEM302 4.3 31.0 1.0 C2C C:HEM302 4.3 28.5 1.0 NE1 C:TRP41 4.4 31.8 1.0 HHC C:HEM302 4.4 39.8 1.0 HHD C:HEM302 4.4 34.2 1.0 HHA C:HEM302 4.4 44.9 1.0 O C:HOH503 4.7 33.6 1.0 CD1 C:TRP41 4.7 28.3 1.0 CH2 C:TRP179 4.9 38.5 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:27.0 occ:1.00 FE D:HEM302 0.0 27.0 1.0 NE2 D:HIS163 2.0 27.7 1.0 NC D:HEM302 2.0 29.4 1.0 NA D:HEM302 2.1 29.7 1.0 NB D:HEM302 2.1 31.7 1.0 ND D:HEM302 2.1 26.4 1.0 O D:HOH470 2.7 34.2 1.0 CD2 D:HIS163 2.9 30.1 1.0 C4B D:HEM302 3.0 32.0 1.0 C1C D:HEM302 3.0 28.8 1.0 C1A D:HEM302 3.0 31.0 1.0 C4D D:HEM302 3.0 27.0 1.0 C4C D:HEM302 3.1 25.4 1.0 C1D D:HEM302 3.1 27.9 1.0 C1B D:HEM302 3.1 34.6 1.0 CE1 D:HIS163 3.1 28.8 1.0 C4A D:HEM302 3.1 29.5 1.0 CHC D:HEM302 3.4 28.5 1.0 CHA D:HEM302 3.4 26.2 1.0 CHD D:HEM302 3.4 25.4 1.0 CHB D:HEM302 3.5 33.5 1.0 CG D:HIS163 4.1 29.2 1.0 ND1 D:HIS163 4.2 26.6 1.0 C3B D:HEM302 4.2 34.0 1.0 NE1 D:TRP41 4.2 23.9 1.0 C3D D:HEM302 4.3 26.8 1.0 C2B D:HEM302 4.3 33.4 1.0 C2A D:HEM302 4.3 31.8 1.0 C2D D:HEM302 4.3 27.8 1.0 C2C D:HEM302 4.3 25.3 1.0 C3C D:HEM302 4.3 25.6 1.0 C3A D:HEM302 4.3 33.9 1.0 O D:HOH515 4.4 33.5 1.0 HHC D:HEM302 4.4 34.1 1.0 O D:HOH519 4.4 33.4 1.0 HHA D:HEM302 4.4 31.4 1.0 HHD D:HEM302 4.4 30.4 1.0 HHB D:HEM302 4.5 40.1 1.0 CD1 D:TRP41 4.7 24.1 1.0 CH2 D:TRP179 4.9 27.9 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:25.9 occ:1.00 FE E:HEM302 0.0 25.9 1.0 NB E:HEM302 2.0 29.2 1.0 NE2 E:HIS163 2.0 24.1 1.0 NC E:HEM302 2.1 29.6 1.0 NA E:HEM302 2.1 31.6 1.0 ND E:HEM302 2.1 26.8 1.0 O E:HOH470 2.4 29.9 1.0 CD2 E:HIS163 2.9 23.6 1.0 C4B E:HEM302 2.9 29.9 1.0 C1B E:HEM302 3.0 32.7 1.0 C1C E:HEM302 3.0 28.7 1.0 C1A E:HEM302 3.1 24.9 1.0 C4D E:HEM302 3.1 31.2 1.0 C1D E:HEM302 3.1 28.9 1.0 C4A E:HEM302 3.1 30.1 1.0 CE1 E:HIS163 3.1 25.6 1.0 C4C E:HEM302 3.1 28.1 1.0 CHC E:HEM302 3.3 32.3 1.0 CHA E:HEM302 3.4 27.6 1.0 CHB E:HEM302 3.5 31.7 1.0 CHD E:HEM302 3.5 28.1 1.0 CG E:HIS163 4.1 26.1 1.0 C3B E:HEM302 4.1 34.8 1.0 ND1 E:HIS163 4.2 24.9 1.0 C2B E:HEM302 4.2 30.6 1.0 NE1 E:TRP41 4.3 31.9 1.0 C2C E:HEM302 4.3 29.2 1.0 C2D E:HEM302 4.3 31.4 1.0 HHC E:HEM302 4.3 38.7 1.0 C3D E:HEM302 4.3 29.9 1.0 C2A E:HEM302 4.3 32.3 1.0 C3A E:HEM302 4.3 30.4 1.0 C3C E:HEM302 4.3 27.6 1.0 O E:HOH463 4.4 34.6 1.0 HHA E:HEM302 4.4 33.0 1.0 HHB E:HEM302 4.4 37.9 1.0 HHD E:HEM302 4.5 33.6 1.0 CD1 E:TRP41 4.5 30.6 1.0 O E:HOH409 4.8 32.6 1.0 CH2 E:TRP179 4.9 29.5 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:35.2 occ:1.00 FE F:HEM302 0.0 35.2 1.0 NC F:HEM302 2.0 37.1 1.0 NA F:HEM302 2.0 38.9 1.0 NB F:HEM302 2.0 35.4 1.0 ND F:HEM302 2.1 37.1 1.0 NE2 F:HIS163 2.2 38.1 1.0 O F:HOH454 2.5 39.1 1.0 CD2 F:HIS163 3.0 36.4 1.0 C1A F:HEM302 3.0 38.7 1.0 C4B F:HEM302 3.0 38.9 1.0 C4C F:HEM302 3.0 31.6 1.0 C1C F:HEM302 3.0 34.5 1.0 C1B F:HEM302 3.0 39.1 1.0 C4A F:HEM302 3.1 39.0 1.0 C4D F:HEM302 3.1 36.1 1.0 C1D F:HEM302 3.1 36.8 1.0 CE1 F:HIS163 3.3 37.3 1.0 CHC F:HEM302 3.4 34.6 1.0 CHA F:HEM302 3.4 38.6 1.0 CHD F:HEM302 3.4 35.1 1.0 CHB F:HEM302 3.4 38.9 1.0 NE1 F:TRP41 4.1 38.7 1.0 CG F:HIS163 4.2 37.9 1.0 C2B F:HEM302 4.2 41.0 1.0 C3B F:HEM302 4.2 39.6 1.0 C2A F:HEM302 4.3 38.2 1.0 C3A F:HEM302 4.3 43.6 1.0 C3C F:HEM302 4.3 38.5 1.0 C2C F:HEM302 4.3 33.4 1.0 C2D F:HEM302 4.3 38.5 1.0 C3D F:HEM302 4.3 36.6 1.0 ND1 F:HIS163 4.3 37.2 1.0 HHC F:HEM302 4.4 41.5 1.0 HHA F:HEM302 4.4 46.3 1.0 HHD F:HEM302 4.4 42.1 1.0 HHB F:HEM302 4.4 46.6 1.0 CD1 F:TRP41 4.5 32.4 1.0 CH2 F:TRP179 4.8 36.1 1.0

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