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Iron in PDB 3fm6: Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii

Enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii

All present enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii:
1.11.1.16;

Protein crystallography data

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii, PDB code: 3fm6 was solved by K.Piontek, A.T.Martinez, T.Choinowski, D.A.Plattner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.32 / 1.13
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 63.333, 63.333, 99.226, 90.00, 90.00, 90.00
R / Rfree (%) 10 / 11.5

Other elements in 3fm6:

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii (pdb code 3fm6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii, PDB code: 3fm6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3fm6

Go back to Iron Binding Sites List in 3fm6
Iron binding site 1 out of 6 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe350

b:4.6
occ:1.00
 FE A:HEM350 0.0 4.6 1.0
NC A:HEM350 2.0 4.6 1.0
NB A:HEM350 2.1 5.0 1.0
NA A:HEM350 2.1 4.4 1.0
ND A:HEM350 2.1 4.6 1.0
NE2 A:HIS169 2.1 4.8 1.0
O A:HOH619 2.6 7.8 1.0
C1C A:HEM350 3.1 4.7 1.0
C1D A:HEM350 3.1 4.3 1.0
C4D A:HEM350 3.1 4.8 1.0
C4A A:HEM350 3.1 4.2 1.0
C4B A:HEM350 3.1 4.8 1.0
C4C A:HEM350 3.1 4.4 1.0
C1B A:HEM350 3.1 4.7 1.0
CE1 A:HIS169 3.1 4.7 1.0
C1A A:HEM350 3.1 4.8 1.0
CD2 A:HIS169 3.2 4.3 1.0
HE1 A:HIS169 3.2 4.6 1.0
HD2 A:HIS169 3.3 4.5 1.0
CHC A:HEM350 3.4 4.8 1.0
CHD A:HEM350 3.4 4.4 1.0
CHB A:HEM350 3.4 4.7 1.0
CHA A:HEM350 3.4 4.6 1.0
HE2 A:PHE186 4.1 5.7 1.0
ND1 A:HIS169 4.2 4.8 1.0
C2D A:HEM350 4.3 4.8 1.0
C3D A:HEM350 4.3 4.7 1.0
C2C A:HEM350 4.3 4.7 1.0
C3B A:HEM350 4.3 4.7 1.0
C3C A:HEM350 4.3 4.7 1.0
C2B A:HEM350 4.3 4.7 1.0
C3A A:HEM350 4.3 4.8 1.0
CG A:HIS169 4.3 4.3 1.0
C2A A:HEM350 4.3 4.7 1.0
HHC A:HEM350 4.4 4.8 1.0
HHD A:HEM350 4.4 4.3 1.0
HHB A:HEM350 4.4 4.6 1.0
HHA A:HEM350 4.4 4.7 1.0
O A:HOH548 4.4 32.8 1.0
HD23 A:LEU166 4.4 5.9 1.0
HD2 A:PHE46 4.5 7.9 1.0
HG3 A:ARG43 4.5 6.0 1.0
HD22 A:LEU166 4.6 5.9 1.0
HE2 A:PHE46 4.7 7.9 1.0
HD11 A:LEU228 4.8 5.6 1.0
CD2 A:LEU166 4.9 6.2 1.0
O A:HOH601 4.9 7.9 1.0
CE2 A:PHE186 5.0 6.1 1.0
HD1 A:HIS169 5.0 4.6 1.0

Iron binding site 2 out of 6 in 3fm6

Go back to Iron Binding Sites List in 3fm6
Iron binding site 2 out of 6 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe334

b:14.9
occ:0.50
 O A:HOH677 1.9 17.5 1.0
O A:HOH454 2.1 32.5 1.0
OD2 A:ASP318 2.1 31.6 1.0
O A:HOH455 2.1 30.6 1.0
NE2 A:HIS293 2.3 15.7 1.0
O A:HOH448 2.4 34.5 1.0
CG A:ASP318 3.2 31.2 1.0
CD2 A:HIS293 3.2 14.5 1.0
HD2 A:HIS293 3.3 14.1 1.0
CE1 A:HIS293 3.3 13.9 1.0
O A:HOH440 3.5 27.0 1.0
OD1 A:ASP318 3.5 31.8 1.0
HE1 A:HIS293 3.6 13.7 1.0
HA A:PRO295 3.9 14.6 1.0
O A:HOH880 4.1 26.5 1.0
O A:HOH778 4.1 28.0 1.0
OG A:SER188 4.2 8.4 1.0
CG A:HIS293 4.3 12.7 1.0
ND1 A:HIS293 4.4 14.1 1.0
HB2 A:SER188 4.4 7.5 1.0
CB A:ASP318 4.5 29.8 1.0
HB2 A:ASP318 4.5 29.7 1.0
H A:ALA296 4.8 16.5 1.0
HB3 A:ASP318 4.8 29.7 1.0
HE21 A:GLN196 4.9 9.4 1.0
CB A:SER188 4.9 7.6 1.0
CA A:PRO295 4.9 15.2 1.0

Iron binding site 3 out of 6 in 3fm6

Go back to Iron Binding Sites List in 3fm6
Iron binding site 3 out of 6 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe338

b:8.9
occ:0.50
 O A:HOH461 1.8 26.8 0.6
O A:HOH462 2.0 15.8 0.5
O A:HOH463 2.0 15.1 0.4
OD1 A:ASP175 2.0 15.2 1.0
OE1 A:GLU83 2.1 9.6 0.4
O A:HOH703 2.2 15.0 0.5
O A:HOH519 2.3 8.1 0.4
O A:HOH675 2.4 10.1 0.6
OE1 A:GLU83 2.6 21.7 0.6
CD A:GLU83 3.0 9.9 0.4
CG A:ASP175 3.1 11.2 1.0
OE2 A:GLU83 3.3 14.4 0.4
HB2 A:ASP175 3.5 9.4 1.0
HB3 A:ASP175 3.5 9.4 1.0
CB A:ASP175 3.6 9.2 1.0
ZN A:ZN336 3.7 13.9 0.4
CD A:GLU83 3.7 18.5 0.6
OE2 A:GLU40 4.0 11.2 0.4
HE2 A:LYS176 4.1 14.5 0.7
OD2 A:ASP175 4.2 13.0 1.0
OE2 A:GLU83 4.3 17.8 0.6
HB2 A:GLU83 4.4 8.7 0.4
O A:HOH834 4.4 22.2 1.0
OE2 A:GLU40 4.4 10.1 0.6
CG A:GLU83 4.4 9.6 0.4
HB3 A:GLU83 4.5 12.5 0.6
HB2 A:GLU83 4.6 12.5 0.6
O A:GLY80 4.7 15.6 1.0
O A:HOH756 4.8 21.7 1.0
CD A:GLU40 4.8 11.3 0.4
CG A:GLU83 4.8 16.1 0.6
CB A:GLU83 4.8 8.5 0.4
CB A:GLU83 4.8 12.6 0.6
HB3 A:GLU83 4.9 8.7 0.4
HA3 A:GLY80 4.9 11.4 1.0
HE2 A:LYS176 4.9 13.6 0.3
HG2 A:GLU83 4.9 9.4 0.4
HA2 A:GLY80 5.0 11.4 1.0
HG3 A:GLU83 5.0 9.4 0.4

Iron binding site 4 out of 6 in 3fm6

Go back to Iron Binding Sites List in 3fm6
Iron binding site 4 out of 6 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe339

b:19.5
occ:0.33
 OD1 A:ASP69 2.1 12.1 1.0
O A:HOH877 2.3 20.9 0.5
O A:HOH666 2.3 6.2 0.3
O A:HOH776 2.4 12.6 0.3
O A:HOH700 2.4 12.0 0.5
HZ1 A:LYS89 2.7 20.2 0.5
HZ3 A:LYS89 2.9 14.0 0.5
HZ2 A:LYS89 3.0 14.0 0.5
CG A:ASP69 3.1 11.2 1.0
HZ2 A:LYS89 3.1 20.2 0.5
NZ A:LYS89 3.3 20.5 0.5
NZ A:LYS89 3.4 13.9 0.5
OD2 A:ASP69 3.4 16.5 1.0
O A:HOH875 3.6 19.9 0.5
H A:THR70 3.8 9.0 1.0
H A:ASP69 3.8 7.3 1.0
HZ3 A:LYS89 3.9 20.2 0.5
OG1 A:THR70 4.0 16.1 1.0
HZ1 A:LYS89 4.0 14.0 0.5
O A:ILE66 4.2 7.4 1.0
HE2 A:LYS89 4.2 13.9 0.5
O A:ALA67 4.2 8.5 1.0
HE3 A:LYS89 4.3 19.4 0.5
CE A:LYS89 4.4 13.9 0.5
CE A:LYS89 4.5 19.9 0.5
CB A:ASP69 4.5 9.6 1.0
N A:ASP69 4.5 7.2 1.0
N A:THR70 4.5 8.9 1.0
HB3 A:ASP69 4.8 9.6 1.0
C A:ALA67 4.8 7.0 1.0
O A:HOH543 4.8 41.0 1.0
CA A:ASP69 4.9 8.1 1.0
HA A:PHE68 4.9 6.6 1.0
HD3 A:LYS89 5.0 13.0 0.5
HD2 A:LYS89 5.0 17.4 0.5
O A:HOH394 5.0 24.8 1.0

Iron binding site 5 out of 6 in 3fm6

Go back to Iron Binding Sites List in 3fm6
Iron binding site 5 out of 6 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe340

b:16.7
occ:0.33
 O A:HOH465 1.7 25.4 0.3
O A:HOH721 2.1 13.3 0.5
O A:HOH679 2.5 31.2 1.0
FE A:FE341 2.5 14.0 0.3
O A:HOH555 2.7 29.1 1.0
HA A:SER98 4.1 7.0 1.0
OD1 A:ASP128 4.1 10.8 1.0
OD2 A:ASP128 4.1 13.5 1.0
O A:HOH843 4.5 23.4 1.0
CG A:ASP128 4.6 9.8 1.0
O A:ILE97 4.6 10.6 1.0
O A:HOH730 4.7 22.3 1.0
O A:HOH475 4.7 46.8 1.0
O A:HOH594 4.7 39.5 1.0
OD1 A:ASN96 4.8 27.9 1.0
CA A:SER98 4.9 7.0 1.0
C A:ILE97 4.9 8.9 1.0

Iron binding site 6 out of 6 in 3fm6

Go back to Iron Binding Sites List in 3fm6
Iron binding site 6 out of 6 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe341

b:14.0
occ:0.33
 O A:HOH555 1.8 29.1 1.0
OD2 A:ASP128 2.0 13.5 1.0
FE A:FE340 2.5 16.7 0.3
O A:HOH843 2.7 23.4 1.0
CG A:ASP128 3.0 9.8 1.0
O A:HOH721 3.0 13.3 0.5
OD1 A:ASP128 3.3 10.8 1.0
O A:HOH715 4.0 18.0 0.5
O A:HOH465 4.1 25.4 0.3
O A:HOH679 4.4 31.2 1.0
CB A:ASP128 4.4 8.0 1.0
HB2 A:ASP128 4.5 8.2 1.0
O A:HOH652 4.7 15.0 1.0
HB3 A:ASP128 4.7 8.2 1.0
O A:HOH594 4.7 39.5 1.0
O A:HOH546 4.9 15.9 1.0

Reference:

K.Piontek, T.Choinowski, M.Perez-Boada, F.J.Ruiz-Duenas, M.J.Martinez, D.A.Plattner, A.T.Martinez. Structural and Site-Directed Mutagenesis Study of Versatile Peroxidase Oxidizing Both Mn(II) and Aromatic Substrates To Be Published.
Page generated: Tue Aug 5 01:12:56 2025

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