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

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

The structure of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum 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 (pdb code 8ff6). 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, PDB code: 8ff6:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:36.7 occ:1.00 FE A:HEM301 0.0 36.7 1.0 NB A:HEM301 1.9 42.4 1.0 NE2 A:HIS163 2.0 39.8 1.0 NC A:HEM301 2.0 38.5 1.0 NA A:HEM301 2.0 42.6 1.0 ND A:HEM301 2.1 38.0 1.0 CD2 A:HIS163 2.9 37.5 1.0 C4B A:HEM301 2.9 41.5 1.0 C1B A:HEM301 2.9 42.9 1.0 C4A A:HEM301 3.0 43.7 1.0 C1C A:HEM301 3.0 37.7 1.0 C4C A:HEM301 3.1 36.4 1.0 C1A A:HEM301 3.1 40.7 1.0 CE1 A:HIS163 3.1 37.0 1.0 C1D A:HEM301 3.1 35.6 1.0 C4D A:HEM301 3.2 39.2 1.0 CHB A:HEM301 3.3 44.1 1.0 CHC A:HEM301 3.4 43.5 1.0 CHD A:HEM301 3.5 35.0 1.0 CHA A:HEM301 3.5 38.8 1.0 O A:HOH424 3.5 59.8 1.0 NE1 A:TRP41 4.0 44.9 1.0 CG A:HIS163 4.1 34.9 1.0 C3B A:HEM301 4.1 40.6 1.0 C2B A:HEM301 4.1 45.8 1.0 ND1 A:HIS163 4.2 32.8 1.0 C2C A:HEM301 4.3 39.8 1.0 C3A A:HEM301 4.3 47.2 1.0 C3C A:HEM301 4.3 38.8 1.0 C2A A:HEM301 4.3 46.0 1.0 CD1 A:TRP41 4.3 37.1 1.0 HHC A:HEM301 4.3 52.1 1.0 HHB A:HEM301 4.3 52.9 1.0 C2D A:HEM301 4.4 31.4 1.0 C3D A:HEM301 4.4 31.5 1.0 HHD A:HEM301 4.5 42.0 1.0 HHA A:HEM301 4.5 46.6 1.0 O A:HOH454 4.8 39.9 1.0 CH2 A:TRP179 5.0 40.0 1.0

Iron 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 Iron with other atoms in the Fe binding site number 2 of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:46.4 occ:1.00 FE B:HEM301 0.0 46.4 1.0 NB B:HEM301 1.9 56.6 1.0 NC B:HEM301 2.0 51.5 1.0 NE2 B:HIS163 2.0 44.0 1.0 NA B:HEM301 2.1 54.4 1.0 ND B:HEM301 2.1 56.4 1.0 C4B B:HEM301 3.0 55.5 1.0 C1B B:HEM301 3.0 53.6 1.0 C4C B:HEM301 3.0 46.1 1.0 CD2 B:HIS163 3.0 47.0 1.0 C1C B:HEM301 3.0 49.1 1.0 CE1 B:HIS163 3.0 45.6 1.0 C4A B:HEM301 3.1 52.4 1.0 C1D B:HEM301 3.1 46.9 1.0 C1A B:HEM301 3.1 53.5 1.0 C4D B:HEM301 3.1 52.3 1.0 CHC B:HEM301 3.4 48.9 1.0 CHB B:HEM301 3.4 54.3 1.0 CHD B:HEM301 3.4 46.0 1.0 CHA B:HEM301 3.5 51.1 1.0 O B:HOH403 3.6 55.0 1.0 NE1 B:TRP41 4.0 52.4 1.0 ND1 B:HIS163 4.1 40.0 1.0 C3B B:HEM301 4.2 56.3 1.0 C2B B:HEM301 4.2 58.8 1.0 CG B:HIS163 4.2 44.8 1.0 C3C B:HEM301 4.2 48.3 1.0 C2C B:HEM301 4.2 49.6 1.0 C3A B:HEM301 4.3 55.9 1.0 C2A B:HEM301 4.3 57.1 1.0 C2D B:HEM301 4.3 49.1 1.0 C3D B:HEM301 4.3 50.5 1.0 CD1 B:TRP41 4.3 46.9 1.0 HHC B:HEM301 4.4 58.7 1.0 HHB B:HEM301 4.4 65.2 1.0 HHD B:HEM301 4.4 55.2 1.0 HHA B:HEM301 4.4 61.4 1.0

Iron 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 Iron with other atoms in the Fe binding site number 3 of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:46.9 occ:1.00 FE C:HEM301 0.0 46.9 1.0 NB C:HEM301 1.9 49.7 1.0 NA C:HEM301 2.0 48.1 1.0 NC C:HEM301 2.1 48.7 1.0 ND C:HEM301 2.1 44.9 1.0 NE2 C:HIS163 2.1 48.6 1.0 C1B C:HEM301 2.9 53.4 1.0 CD2 C:HIS163 2.9 44.7 1.0 C4B C:HEM301 2.9 55.6 1.0 C4A C:HEM301 3.0 48.0 1.0 C1C C:HEM301 3.1 48.4 1.0 C1D C:HEM301 3.1 46.6 1.0 C4C C:HEM301 3.1 44.3 1.0 C1A C:HEM301 3.1 46.6 1.0 C4D C:HEM301 3.2 44.4 1.0 CHB C:HEM301 3.3 51.1 1.0 CE1 C:HIS163 3.3 44.3 1.0 O C:HOH406 3.3 49.2 1.0 CHC C:HEM301 3.4 51.2 1.0 CHD C:HEM301 3.5 44.5 1.0 CHA C:HEM301 3.5 46.4 1.0 C2B C:HEM301 4.1 57.4 1.0 C3B C:HEM301 4.1 57.5 1.0 CG C:HIS163 4.1 41.3 1.0 NE1 C:TRP41 4.2 46.5 1.0 C3A C:HEM301 4.2 54.3 1.0 HHB C:HEM301 4.2 61.3 1.0 ND1 C:HIS163 4.3 39.1 1.0 C2A C:HEM301 4.3 53.9 1.0 C2C C:HEM301 4.3 48.4 1.0 C3C C:HEM301 4.3 48.4 1.0 C2D C:HEM301 4.3 48.2 1.0 C3D C:HEM301 4.4 41.5 1.0 HHC C:HEM301 4.4 61.4 1.0 HHD C:HEM301 4.5 53.4 1.0 CD1 C:TRP41 4.5 44.7 1.0 HHA C:HEM301 4.5 55.6 1.0 O C:HOH436 4.6 47.2 1.0 CH2 C:TRP179 5.0 47.5 1.0

Iron 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 Iron with other atoms in the Fe binding site number 4 of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:47.6 occ:1.00 FE D:HEM301 0.0 47.6 1.0 NE2 D:HIS163 2.0 47.0 1.0 NB D:HEM301 2.0 52.6 1.0 NC D:HEM301 2.0 51.3 1.0 NA D:HEM301 2.1 54.2 1.0 ND D:HEM301 2.1 47.6 1.0 O D:HOH406 2.7 47.0 1.0 CD2 D:HIS163 2.8 47.8 1.0 C4B D:HEM301 3.0 51.8 1.0 C1B D:HEM301 3.0 54.0 1.0 C1C D:HEM301 3.0 51.2 1.0 CE1 D:HIS163 3.0 50.0 1.0 C1A D:HEM301 3.0 51.6 1.0 C4D D:HEM301 3.1 47.1 1.0 C4A D:HEM301 3.1 47.8 1.0 C4C D:HEM301 3.1 45.5 1.0 C1D D:HEM301 3.1 46.3 1.0 CHC D:HEM301 3.4 49.1 1.0 CHA D:HEM301 3.4 48.1 1.0 CHB D:HEM301 3.4 49.3 1.0 CHD D:HEM301 3.5 43.7 1.0 O D:HOH430 3.7 48.6 1.0 CG D:HIS163 4.0 48.0 1.0 ND1 D:HIS163 4.1 44.5 1.0 NE1 D:TRP41 4.1 45.0 1.0 C3B D:HEM301 4.2 55.7 1.0 C2B D:HEM301 4.2 54.8 1.0 C2C D:HEM301 4.3 48.6 1.0 C2A D:HEM301 4.3 52.8 1.0 C3A D:HEM301 4.3 52.6 1.0 C3D D:HEM301 4.3 47.5 1.0 C3C D:HEM301 4.3 46.9 1.0 C2D D:HEM301 4.3 43.5 1.0 HHC D:HEM301 4.3 59.0 1.0 CD1 D:TRP41 4.4 43.2 1.0 HHA D:HEM301 4.4 57.7 1.0 HHB D:HEM301 4.4 59.1 1.0 HHD D:HEM301 4.5 52.5 1.0 O D:HOH453 5.0 50.2 1.0

Iron 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 Iron with other atoms in the Fe binding site number 5 of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:47.4 occ:1.00 FE E:HEM301 0.0 47.4 1.0 NB E:HEM301 1.9 50.5 1.0 NE2 E:HIS163 2.0 46.5 1.0 NC E:HEM301 2.0 52.3 1.0 NA E:HEM301 2.1 56.8 1.0 ND E:HEM301 2.1 48.1 1.0 C4B E:HEM301 2.8 57.1 1.0 CD2 E:HIS163 2.8 46.7 1.0 C1B E:HEM301 2.9 54.8 1.0 C1C E:HEM301 3.0 49.4 1.0 CE1 E:HIS163 3.1 49.4 1.0 C4A E:HEM301 3.1 54.0 1.0 C4C E:HEM301 3.1 47.4 1.0 C1D E:HEM301 3.1 51.1 1.0 C4D E:HEM301 3.1 50.5 1.0 C1A E:HEM301 3.1 52.1 1.0 O E:HOH405 3.2 50.9 1.0 CHC E:HEM301 3.3 54.9 1.0 CHB E:HEM301 3.4 58.0 1.0 CHD E:HEM301 3.5 49.7 1.0 CHA E:HEM301 3.5 54.5 1.0 C3B E:HEM301 4.0 57.8 1.0 C2B E:HEM301 4.0 58.0 1.0 CG E:HIS163 4.0 47.7 1.0 NE1 E:TRP41 4.1 51.1 1.0 ND1 E:HIS163 4.1 47.0 1.0 C2C E:HEM301 4.3 50.8 1.0 HHC E:HEM301 4.3 65.8 1.0 CD1 E:TRP41 4.3 49.5 1.0 C2D E:HEM301 4.3 49.1 1.0 C3C E:HEM301 4.3 46.8 1.0 C3D E:HEM301 4.3 49.8 1.0 C3A E:HEM301 4.3 58.7 1.0 C2A E:HEM301 4.3 58.9 1.0 HHB E:HEM301 4.3 69.6 1.0 HHD E:HEM301 4.5 59.6 1.0 HHA E:HEM301 4.5 65.4 1.0 CH2 E:TRP179 4.9 51.8 1.0

Iron 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 Iron with other atoms in the Fe binding site number 6 of Cytosolic Ascorbate Peroxidase Mutant From Panicum Virgatum within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe301 b:57.7 occ:1.00 FE F:HEM301 0.0 57.7 1.0 NE2 F:HIS163 2.0 57.4 1.0 NC F:HEM301 2.0 63.0 1.0 NB F:HEM301 2.0 66.2 1.0 ND F:HEM301 2.1 62.1 1.0 NA F:HEM301 2.1 68.3 1.0 CD2 F:HIS163 2.8 55.6 1.0 C1B F:HEM301 3.0 68.2 1.0 C4C F:HEM301 3.0 61.5 1.0 C4B F:HEM301 3.1 69.8 1.0 C1C F:HEM301 3.1 64.6 1.0 C1D F:HEM301 3.1 60.5 1.0 C4A F:HEM301 3.1 68.7 1.0 C4D F:HEM301 3.1 59.2 1.0 C1A F:HEM301 3.1 63.7 1.0 CE1 F:HIS163 3.1 59.6 1.0 CHD F:HEM301 3.4 58.7 1.0 CHC F:HEM301 3.4 63.7 1.0 CHB F:HEM301 3.4 67.8 1.0 CHA F:HEM301 3.5 63.6 1.0 CG F:HIS163 4.0 55.0 1.0 ND1 F:HIS163 4.1 56.3 1.0 C2B F:HEM301 4.2 72.4 1.0 C3B F:HEM301 4.3 70.6 1.0 C2C F:HEM301 4.3 63.2 1.0 C3C F:HEM301 4.3 59.7 1.0 C3A F:HEM301 4.3 67.4 1.0 C2D F:HEM301 4.3 61.4 1.0 C2A F:HEM301 4.3 67.7 1.0 C3D F:HEM301 4.3 56.3 1.0 NE1 F:TRP41 4.3 60.9 1.0 HHD F:HEM301 4.4 70.5 1.0 HHC F:HEM301 4.4 76.5 1.0 HHB F:HEM301 4.4 81.3 1.0 CD1 F:TRP41 4.4 58.9 1.0 HHA F:HEM301 4.5 76.4 1.0 CH2 F:TRP179 4.8 56.6 1.0 CZ2 F:TRP179 4.9 57.5 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