Atomistry » Iron » PDB 6yf4-6zae » 6yr4
Atomistry »
  Iron »
    PDB 6yf4-6zae »
      6yr4 »

Iron in PDB 6yr4: Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure

Protein crystallography data

The structure of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure, PDB code: 6yr4 was solved by M.Lucic, F.S.N.Dworkowski, J.A.R.Worrall, M.A.Hough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.61 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.35, 119.91, 194.15, 90, 90, 90
R / Rfree (%) 18.8 / 23.2

Other elements in 6yr4:

The structure of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure (pdb code 6yr4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure, PDB code: 6yr4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6yr4

Go back to Iron Binding Sites List in 6yr4
Iron binding site 1 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.5
occ:1.00
FE A:HEM401 0.0 18.5 1.0
O A:O403 1.7 17.5 1.0
ND A:HEM401 1.9 18.1 1.0
NA A:HEM401 2.0 19.4 1.0
NC A:HEM401 2.1 17.7 1.0
NB A:HEM401 2.1 18.3 1.0
NE2 A:HIS225 2.1 21.2 1.0
C1D A:HEM401 2.9 18.5 1.0
C4D A:HEM401 2.9 19.1 1.0
CD2 A:HIS225 3.0 20.9 1.0
C1A A:HEM401 3.0 18.3 1.0
C1B A:HEM401 3.0 18.2 1.0
C4A A:HEM401 3.0 18.8 1.0
C4C A:HEM401 3.0 18.4 1.0
C4B A:HEM401 3.1 20.6 1.0
C1C A:HEM401 3.1 18.6 1.0
CE1 A:HIS225 3.2 18.3 1.0
CHB A:HEM401 3.4 17.6 1.0
CHA A:HEM401 3.4 18.6 1.0
CHD A:HEM401 3.4 17.9 1.0
CHC A:HEM401 3.5 18.0 1.0
NH1 A:ARG243 3.9 19.0 1.0
CG A:HIS225 4.2 19.0 1.0
C2A A:HEM401 4.2 19.7 1.0
C2D A:HEM401 4.2 19.3 1.0
C3A A:HEM401 4.2 19.9 1.0
C3D A:HEM401 4.2 20.0 1.0
ND1 A:HIS225 4.2 19.7 1.0
C2B A:HEM401 4.2 19.3 1.0
ND2 A:ASN245 4.3 22.6 1.0
C3C A:HEM401 4.3 19.8 1.0
C2C A:HEM401 4.3 18.5 1.0
C3B A:HEM401 4.3 21.6 1.0
CD A:ARG243 4.5 19.2 1.0
CZ A:ARG243 4.7 20.2 1.0
NE A:ARG243 4.8 19.0 1.0

Iron binding site 2 out of 6 in 6yr4

Go back to Iron Binding Sites List in 6yr4
Iron binding site 2 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:20.4
occ:1.00
FE B:HEM401 0.0 20.4 1.0
O B:O402 1.8 24.3 1.0
ND B:HEM401 1.9 18.4 1.0
NA B:HEM401 2.0 18.5 1.0
NB B:HEM401 2.1 19.3 1.0
NC B:HEM401 2.1 19.3 1.0
NE2 B:HIS225 2.2 18.8 1.0
C1D B:HEM401 2.9 18.2 1.0
C4D B:HEM401 2.9 18.6 1.0
C4B B:HEM401 3.0 19.3 1.0
C1A B:HEM401 3.0 19.2 1.0
C4C B:HEM401 3.1 19.0 1.0
C1B B:HEM401 3.1 19.8 1.0
C1C B:HEM401 3.1 18.9 1.0
C4A B:HEM401 3.1 20.1 1.0
CE1 B:HIS225 3.1 20.9 1.0
CD2 B:HIS225 3.2 20.1 1.0
CHA B:HEM401 3.4 19.7 1.0
CHD B:HEM401 3.4 18.6 1.0
CHC B:HEM401 3.4 18.5 1.0
CHB B:HEM401 3.5 19.1 1.0
NH1 B:ARG243 3.9 25.9 1.0
C2D B:HEM401 4.1 18.4 1.0
C3D B:HEM401 4.2 19.3 1.0
ND2 B:ASN245 4.2 26.9 1.0
ND1 B:HIS225 4.2 21.6 1.0
C2A B:HEM401 4.2 19.0 1.0
C3A B:HEM401 4.3 18.7 1.0
CD B:ARG243 4.3 23.6 1.0
C2C B:HEM401 4.3 19.5 1.0
C3B B:HEM401 4.3 20.5 1.0
C3C B:HEM401 4.3 19.1 1.0
C2B B:HEM401 4.3 20.1 1.0
CG B:HIS225 4.3 18.8 1.0
CZ B:ARG243 4.7 24.6 1.0
NE B:ARG243 4.8 23.4 1.0

Iron binding site 3 out of 6 in 6yr4

Go back to Iron Binding Sites List in 6yr4
Iron binding site 3 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:21.1
occ:1.00
FE C:HEM401 0.0 21.1 1.0
O C:O403 1.7 20.1 1.0
ND C:HEM401 1.9 20.9 1.0
NA C:HEM401 2.0 22.5 1.0
NC C:HEM401 2.1 18.4 1.0
NB C:HEM401 2.1 20.5 1.0
NE2 C:HIS225 2.1 20.4 1.0
C1D C:HEM401 2.9 19.4 1.0
C4D C:HEM401 2.9 18.7 1.0
C1A C:HEM401 3.0 19.1 1.0
C4A C:HEM401 3.0 21.0 1.0
C4C C:HEM401 3.0 19.4 1.0
CD2 C:HIS225 3.0 23.3 1.0
C1B C:HEM401 3.0 21.6 1.0
C4B C:HEM401 3.1 20.9 1.0
C1C C:HEM401 3.1 19.1 1.0
CE1 C:HIS225 3.2 22.2 1.0
CHA C:HEM401 3.4 19.8 1.0
CHD C:HEM401 3.4 18.1 1.0
CHB C:HEM401 3.4 20.7 1.0
CHC C:HEM401 3.5 18.2 1.0
NH1 C:ARG243 3.9 21.6 1.0
C2A C:HEM401 4.2 20.1 1.0
C3A C:HEM401 4.2 19.5 1.0
C2D C:HEM401 4.2 18.9 1.0
CG C:HIS225 4.2 23.1 1.0
C3D C:HEM401 4.2 19.6 1.0
C3C C:HEM401 4.2 18.2 1.0
ND1 C:HIS225 4.2 22.5 1.0
C2B C:HEM401 4.3 20.5 1.0
ND2 C:ASN245 4.3 20.9 1.0
C2C C:HEM401 4.3 18.4 1.0
C3B C:HEM401 4.3 21.6 1.0
CD C:ARG243 4.5 22.8 1.0
CZ C:ARG243 4.7 21.7 1.0
NE C:ARG243 4.9 21.8 1.0

Iron binding site 4 out of 6 in 6yr4

Go back to Iron Binding Sites List in 6yr4
Iron binding site 4 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:17.1
occ:1.00
FE D:HEM401 0.0 17.1 1.0
O D:O403 1.8 18.1 1.0
ND D:HEM401 1.9 16.3 1.0
NA D:HEM401 2.0 17.0 1.0
NC D:HEM401 2.0 17.2 1.0
NB D:HEM401 2.0 18.3 1.0
NE2 D:HIS225 2.2 19.6 1.0
C1D D:HEM401 2.9 16.5 1.0
C4D D:HEM401 3.0 16.6 1.0
C4B D:HEM401 3.0 18.0 1.0
C1A D:HEM401 3.0 16.4 1.0
C4C D:HEM401 3.0 17.2 1.0
C1B D:HEM401 3.0 18.7 1.0
C4A D:HEM401 3.0 18.6 1.0
C1C D:HEM401 3.1 17.1 1.0
CD2 D:HIS225 3.1 18.8 1.0
CE1 D:HIS225 3.2 19.8 1.0
CHD D:HEM401 3.4 17.3 1.0
CHC D:HEM401 3.4 16.6 1.0
CHA D:HEM401 3.4 16.4 1.0
CHB D:HEM401 3.4 18.4 1.0
NH1 D:ARG243 3.9 17.4 1.0
C2D D:HEM401 4.2 17.5 1.0
ND2 D:ASN245 4.2 24.8 1.0
C2A D:HEM401 4.2 17.1 1.0
C3D D:HEM401 4.2 17.0 1.0
C3A D:HEM401 4.2 18.2 1.0
C2C D:HEM401 4.2 15.6 1.0
C3C D:HEM401 4.2 16.4 1.0
C3B D:HEM401 4.2 17.8 1.0
C2B D:HEM401 4.2 18.7 1.0
CG D:HIS225 4.3 18.4 1.0
ND1 D:HIS225 4.3 19.9 1.0
CD D:ARG243 4.4 19.9 1.0
CZ D:ARG243 4.6 17.4 1.0
NE D:ARG243 4.8 19.4 1.0

Iron binding site 5 out of 6 in 6yr4

Go back to Iron Binding Sites List in 6yr4
Iron binding site 5 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:21.7
occ:1.00
FE E:HEM401 0.0 21.7 1.0
O E:O402 1.8 21.4 1.0
ND E:HEM401 1.9 20.6 1.0
NA E:HEM401 2.0 19.2 1.0
NB E:HEM401 2.1 20.6 1.0
NC E:HEM401 2.1 21.6 1.0
NE2 E:HIS225 2.1 20.3 1.0
C1D E:HEM401 2.9 22.6 1.0
C4D E:HEM401 2.9 21.3 1.0
C4C E:HEM401 3.0 20.0 1.0
C1B E:HEM401 3.0 21.0 1.0
C4B E:HEM401 3.0 20.6 1.0
C1A E:HEM401 3.0 20.7 1.0
C4A E:HEM401 3.0 20.7 1.0
CE1 E:HIS225 3.1 22.0 1.0
C1C E:HEM401 3.1 20.2 1.0
CD2 E:HIS225 3.1 20.0 1.0
CHD E:HEM401 3.3 21.4 1.0
CHA E:HEM401 3.4 20.2 1.0
CHB E:HEM401 3.4 18.4 1.0
CHC E:HEM401 3.5 21.0 1.0
NH1 E:ARG243 3.9 23.6 1.0
ND2 E:ASN245 4.2 25.4 1.0
C2D E:HEM401 4.2 21.8 1.0
C3D E:HEM401 4.2 21.2 1.0
ND1 E:HIS225 4.2 20.4 1.0
C2B E:HEM401 4.2 21.0 1.0
C3A E:HEM401 4.2 20.4 1.0
C3B E:HEM401 4.2 23.0 1.0
CG E:HIS225 4.2 21.2 1.0
C3C E:HEM401 4.2 20.3 1.0
C2A E:HEM401 4.3 20.9 1.0
C2C E:HEM401 4.3 21.8 1.0
CD E:ARG243 4.4 21.9 1.0
CZ E:ARG243 4.7 22.3 1.0
NE E:ARG243 4.9 23.0 1.0

Iron binding site 6 out of 6 in 6yr4

Go back to Iron Binding Sites List in 6yr4
Iron binding site 6 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:20.3
occ:1.00
FE F:HEM401 0.0 20.3 1.0
O F:O402 1.7 20.6 1.0
ND F:HEM401 1.9 19.9 1.0
NA F:HEM401 2.0 18.4 1.0
NB F:HEM401 2.1 18.6 1.0
NE2 F:HIS225 2.1 18.6 1.0
NC F:HEM401 2.1 20.2 1.0
C1D F:HEM401 2.9 20.5 1.0
C4D F:HEM401 2.9 20.1 1.0
C1A F:HEM401 3.0 20.0 1.0
C4B F:HEM401 3.0 20.1 1.0
CE1 F:HIS225 3.0 21.6 1.0
C4A F:HEM401 3.0 19.6 1.0
C1B F:HEM401 3.1 19.4 1.0
CD2 F:HIS225 3.1 20.7 1.0
C4C F:HEM401 3.1 20.3 1.0
C1C F:HEM401 3.1 19.6 1.0
CHA F:HEM401 3.3 20.2 1.0
CHD F:HEM401 3.4 19.1 1.0
CHC F:HEM401 3.4 17.8 1.0
CHB F:HEM401 3.5 17.8 1.0
NH1 F:ARG243 3.9 21.6 1.0
ND1 F:HIS225 4.1 20.2 1.0
CG F:HIS225 4.2 20.0 1.0
C2D F:HEM401 4.2 19.8 1.0
C2A F:HEM401 4.2 18.2 1.0
C3D F:HEM401 4.2 20.1 1.0
C3A F:HEM401 4.2 18.7 1.0
C3B F:HEM401 4.3 18.7 1.0
C2B F:HEM401 4.3 18.2 1.0
ND2 F:ASN245 4.3 22.1 1.0
C3C F:HEM401 4.3 20.1 1.0
C2C F:HEM401 4.3 20.1 1.0
CD F:ARG243 4.4 20.9 1.0
CZ F:ARG243 4.7 22.0 1.0
NE F:ARG243 4.9 20.6 1.0

Reference:

M.Lucic, D.A.Svistunenko, M.T.Wilson, A.K.Chaplin, B.Davy, A.Ebrahim, D.Axford, T.Tosha, H.Sugimoto, S.Owada, F.S.N.Dworkowski, I.Tews, R.L.Owen, M.A.Hough, J.A.R.Worrall. Serial Femtosecond Zero Dose Crystallography Captures A Water-Free Distal Heme Site in A Dye-Decolorising Peroxidase to Reveal A Catalytic Role For An Arginine in Fe IV =O Formation. Angew.Chem.Int.Ed.Engl. V. 59 21656 2020.
ISSN: ESSN 1521-3773
PubMed: 32780931
DOI: 10.1002/ANIE.202008622
Page generated: Wed Aug 7 16:41:49 2024

Last articles

Zn in 1MC5
Zn in 1MFM
Zn in 1MA0
Zn in 1MED
Zn in 1MEA
Zn in 1MBX
Zn in 1MA3
Zn in 1M9O
Zn in 1M9R
Zn in 1M9Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy