Iron in PDB 6yrd: Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State

Protein crystallography data

The structure of Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State, PDB code: 6yrd was solved by M.Lucic, D.A.Axford, R.L.Owen, 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) 13.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.3, 120, 198.45, 90, 90, 90
R / Rfree (%) 16.7 / 19.9

Other elements in 6yrd:

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

Magnesium (Mg) 2 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 6yrd

Go back to Iron Binding Sites List in 6yrd
Iron binding site 1 out of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State


Mono view


Stereo pair view

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

b:22.9
occ:1.00
FE A:HEM401 0.0 22.9 1.0
O A:O403 1.7 26.3 1.0
ND A:HEM401 2.0 22.7 1.0
NA A:HEM401 2.0 22.5 1.0
NB A:HEM401 2.0 23.9 1.0
NC A:HEM401 2.1 22.8 1.0
NE2 A:HIS225 2.1 22.9 1.0
C1B A:HEM401 3.0 23.2 1.0
C4D A:HEM401 3.0 21.9 1.0
C1D A:HEM401 3.0 23.9 1.0
C4A A:HEM401 3.0 23.4 1.0
C1A A:HEM401 3.0 22.5 1.0
C4B A:HEM401 3.0 24.7 1.0
CD2 A:HIS225 3.1 24.7 1.0
C4C A:HEM401 3.1 25.2 1.0
C1C A:HEM401 3.1 23.8 1.0
CE1 A:HIS225 3.1 24.1 1.0
CHB A:HEM401 3.4 23.3 1.0
CHA A:HEM401 3.4 22.3 1.0
CHD A:HEM401 3.4 23.8 1.0
CHC A:HEM401 3.5 23.1 1.0
NH1 A:ARG243 4.0 24.5 1.0
C2B A:HEM401 4.2 24.6 1.0
CG A:HIS225 4.2 24.3 1.0
ND1 A:HIS225 4.2 22.9 1.0
C3A A:HEM401 4.2 22.5 1.0
C2D A:HEM401 4.2 22.9 1.0
C3B A:HEM401 4.2 23.9 1.0
C2A A:HEM401 4.2 22.9 1.0
C3D A:HEM401 4.2 21.5 1.0
C2C A:HEM401 4.3 25.0 1.0
C3C A:HEM401 4.3 24.4 1.0
ND2 A:ASN245 4.4 28.1 1.0
CD A:ARG243 4.4 25.0 1.0
CZ A:ARG243 4.7 27.1 1.0
NE A:ARG243 4.9 26.4 1.0

Iron binding site 2 out of 6 in 6yrd

Go back to Iron Binding Sites List in 6yrd
Iron binding site 2 out of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State


Mono view


Stereo pair view

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

b:26.4
occ:1.00
FE B:HEM401 0.0 26.4 1.0
O B:O402 1.9 30.1 1.0
ND B:HEM401 2.0 26.6 1.0
NA B:HEM401 2.0 24.1 1.0
NC B:HEM401 2.0 24.7 1.0
NB B:HEM401 2.1 25.8 1.0
NE2 B:HIS225 2.1 24.3 1.0
C1D B:HEM401 2.9 24.8 1.0
C4D B:HEM401 3.0 26.3 1.0
C4C B:HEM401 3.0 26.3 1.0
C1A B:HEM401 3.0 23.0 1.0
C4B B:HEM401 3.0 25.4 1.0
C1C B:HEM401 3.0 23.4 1.0
C4A B:HEM401 3.0 23.8 1.0
C1B B:HEM401 3.1 24.4 1.0
CD2 B:HIS225 3.1 25.6 1.0
CE1 B:HIS225 3.1 28.8 1.0
CHD B:HEM401 3.3 25.0 1.0
CHC B:HEM401 3.4 26.0 1.0
CHA B:HEM401 3.4 24.5 1.0
CHB B:HEM401 3.5 24.7 1.0
NH1 B:ARG243 4.0 26.8 1.0
C3C B:HEM401 4.2 25.0 1.0
C2C B:HEM401 4.2 25.4 1.0
C2D B:HEM401 4.2 24.7 1.0
C2A B:HEM401 4.2 26.5 1.0
ND1 B:HIS225 4.2 25.5 1.0
CG B:HIS225 4.2 23.9 1.0
C3A B:HEM401 4.2 25.7 1.0
C3D B:HEM401 4.2 26.7 1.0
C3B B:HEM401 4.3 25.7 1.0
C2B B:HEM401 4.3 24.9 1.0
ND2 B:ASN245 4.3 30.6 1.0
CD B:ARG243 4.4 27.9 1.0
CZ B:ARG243 4.7 27.6 1.0
NE B:ARG243 4.8 27.8 1.0

Iron binding site 3 out of 6 in 6yrd

Go back to Iron Binding Sites List in 6yrd
Iron binding site 3 out of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State


Mono view


Stereo pair view

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

b:26.5
occ:1.00
FE C:HEM401 0.0 26.5 1.0
O C:O403 1.9 29.2 1.0
ND C:HEM401 2.0 24.3 1.0
NA C:HEM401 2.0 26.1 1.0
NB C:HEM401 2.0 26.5 1.0
NC C:HEM401 2.0 25.2 1.0
NE2 C:HIS225 2.1 26.4 1.0
C4B C:HEM401 3.0 26.9 1.0
C4D C:HEM401 3.0 24.9 1.0
C1B C:HEM401 3.0 27.1 1.0
C1D C:HEM401 3.0 25.3 1.0
C4A C:HEM401 3.0 27.0 1.0
C1A C:HEM401 3.0 26.3 1.0
C4C C:HEM401 3.0 26.2 1.0
C1C C:HEM401 3.1 26.2 1.0
CD2 C:HIS225 3.1 28.2 1.0
CE1 C:HIS225 3.1 26.8 1.0
CHB C:HEM401 3.4 25.9 1.0
CHC C:HEM401 3.4 25.0 1.0
CHD C:HEM401 3.4 25.0 1.0
CHA C:HEM401 3.4 26.4 1.0
NH1 C:ARG243 3.9 27.1 1.0
C3B C:HEM401 4.2 26.6 1.0
C3A C:HEM401 4.2 27.1 1.0
ND1 C:HIS225 4.2 26.0 1.0
C2A C:HEM401 4.2 26.8 1.0
C2B C:HEM401 4.2 24.8 1.0
CG C:HIS225 4.2 27.3 1.0
C3D C:HEM401 4.2 26.6 1.0
C3C C:HEM401 4.2 25.1 1.0
C2C C:HEM401 4.3 26.5 1.0
C2D C:HEM401 4.3 25.5 1.0
ND2 C:ASN245 4.3 28.9 1.0
CD C:ARG243 4.4 28.6 1.0
CZ C:ARG243 4.7 29.5 1.0
NE C:ARG243 4.9 27.7 1.0

Iron binding site 4 out of 6 in 6yrd

Go back to Iron Binding Sites List in 6yrd
Iron binding site 4 out of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State


Mono view


Stereo pair view

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

b:23.2
occ:1.00
FE D:HEM401 0.0 23.2 1.0
O D:O403 1.9 27.3 1.0
ND D:HEM401 1.9 22.9 1.0
NA D:HEM401 2.0 22.1 1.0
NB D:HEM401 2.1 24.8 1.0
NC D:HEM401 2.1 21.8 1.0
NE2 D:HIS225 2.1 22.8 1.0
C1D D:HEM401 3.0 22.3 1.0
C4D D:HEM401 3.0 22.7 1.0
C1A D:HEM401 3.0 23.5 1.0
C4B D:HEM401 3.0 25.7 1.0
C4C D:HEM401 3.0 21.7 1.0
C4A D:HEM401 3.0 23.1 1.0
C1B D:HEM401 3.1 23.0 1.0
C1C D:HEM401 3.1 22.3 1.0
CE1 D:HIS225 3.1 24.0 1.0
CD2 D:HIS225 3.1 23.8 1.0
CHD D:HEM401 3.4 22.6 1.0
CHA D:HEM401 3.4 23.6 1.0
CHC D:HEM401 3.4 23.6 1.0
CHB D:HEM401 3.5 21.9 1.0
NH1 D:ARG243 4.0 25.6 1.0
ND1 D:HIS225 4.2 21.9 1.0
CG D:HIS225 4.2 23.4 1.0
C2A D:HEM401 4.2 23.2 1.0
C3A D:HEM401 4.2 22.0 1.0
C2C D:HEM401 4.2 23.2 1.0
C2D D:HEM401 4.2 22.7 1.0
C3D D:HEM401 4.2 24.1 1.0
C3C D:HEM401 4.3 22.2 1.0
C2B D:HEM401 4.3 25.0 1.0
C3B D:HEM401 4.3 25.0 1.0
ND2 D:ASN245 4.3 29.2 1.0
CD D:ARG243 4.4 27.9 1.0
CZ D:ARG243 4.7 25.7 1.0
NE D:ARG243 4.8 26.3 1.0

Iron binding site 5 out of 6 in 6yrd

Go back to Iron Binding Sites List in 6yrd
Iron binding site 5 out of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State


Mono view


Stereo pair view

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

b:26.9
occ:1.00
FE E:HEM401 0.0 26.9 1.0
O E:O402 1.8 31.8 1.0
ND E:HEM401 1.9 25.7 1.0
NA E:HEM401 2.0 25.1 1.0
NB E:HEM401 2.0 27.0 1.0
NE2 E:HIS225 2.1 26.8 1.0
NC E:HEM401 2.1 26.0 1.0
C4D E:HEM401 2.9 27.4 1.0
C1D E:HEM401 3.0 27.7 1.0
C1A E:HEM401 3.0 26.0 1.0
C1B E:HEM401 3.0 26.8 1.0
C4A E:HEM401 3.0 27.2 1.0
C4B E:HEM401 3.0 28.1 1.0
CE1 E:HIS225 3.0 30.6 1.0
C4C E:HEM401 3.0 27.0 1.0
C1C E:HEM401 3.1 26.7 1.0
CD2 E:HIS225 3.1 26.5 1.0
CHA E:HEM401 3.4 27.2 1.0
CHB E:HEM401 3.4 27.0 1.0
CHD E:HEM401 3.4 28.2 1.0
CHC E:HEM401 3.4 25.3 1.0
NH1 E:ARG243 3.9 29.2 1.0
ND1 E:HIS225 4.2 28.0 1.0
C2D E:HEM401 4.2 28.1 1.0
C3D E:HEM401 4.2 27.6 1.0
CG E:HIS225 4.2 28.1 1.0
C2B E:HEM401 4.2 27.1 1.0
C2A E:HEM401 4.2 26.8 1.0
C3A E:HEM401 4.2 25.7 1.0
C3C E:HEM401 4.2 26.5 1.0
C2C E:HEM401 4.3 25.9 1.0
ND2 E:ASN245 4.3 29.6 1.0
C3B E:HEM401 4.3 26.7 1.0
CD E:ARG243 4.4 30.1 1.0
CZ E:ARG243 4.7 28.2 1.0
NE E:ARG243 4.8 30.4 1.0

Iron binding site 6 out of 6 in 6yrd

Go back to Iron Binding Sites List in 6yrd
Iron binding site 6 out of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State


Mono view


Stereo pair view

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

b:24.9
occ:1.00
FE F:HEM401 0.0 24.9 1.0
O F:O402 1.8 26.9 1.0
ND F:HEM401 1.9 23.8 1.0
NA F:HEM401 2.0 23.8 1.0
NB F:HEM401 2.0 25.4 1.0
NC F:HEM401 2.1 25.3 1.0
NE2 F:HIS225 2.1 23.8 1.0
C1D F:HEM401 3.0 24.6 1.0
C4D F:HEM401 3.0 25.1 1.0
C1A F:HEM401 3.0 24.6 1.0
C4A F:HEM401 3.0 23.0 1.0
C1B F:HEM401 3.0 26.6 1.0
C4B F:HEM401 3.0 26.8 1.0
C4C F:HEM401 3.0 25.9 1.0
CE1 F:HIS225 3.1 26.0 1.0
C1C F:HEM401 3.1 25.4 1.0
CD2 F:HIS225 3.1 24.2 1.0
CHB F:HEM401 3.4 24.1 1.0
CHD F:HEM401 3.4 26.3 1.0
CHA F:HEM401 3.4 24.3 1.0
CHC F:HEM401 3.4 23.9 1.0
NH1 F:ARG243 3.9 25.1 1.0
C3A F:HEM401 4.2 22.6 1.0
C2A F:HEM401 4.2 24.4 1.0
ND1 F:HIS225 4.2 25.7 1.0
C2D F:HEM401 4.2 24.6 1.0
C3D F:HEM401 4.2 23.6 1.0
CG F:HIS225 4.2 24.6 1.0
C2B F:HEM401 4.3 25.8 1.0
C3C F:HEM401 4.3 27.1 1.0
C2C F:HEM401 4.3 25.0 1.0
C3B F:HEM401 4.3 25.4 1.0
ND2 F:ASN245 4.3 27.0 1.0
CD F:ARG243 4.4 26.8 1.0
CZ F:ARG243 4.7 26.2 1.0
NE F:ARG243 4.8 26.4 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: Sun Jan 24 17:08:45 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy