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Iron in PDB 6yrc: Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State

Protein crystallography data

The structure of Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State, PDB code: 6yrc 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) 49.05 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.79, 120.27, 196.01, 90, 90, 90
R / Rfree (%) 17.6 / 21.8

Other elements in 6yrc:

The structure of Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 6yrc

Go back to Iron Binding Sites List in 6yrc
Iron binding site 1 out of 6 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

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

b:24.8
occ:1.00
FE A:HEM401 0.0 24.8 1.0
ND A:HEM401 2.0 25.5 1.0
NA A:HEM401 2.0 23.6 1.0
NB A:HEM401 2.1 24.4 1.0
NC A:HEM401 2.1 23.3 1.0
NE2 A:HIS225 2.1 22.1 1.0
C4D A:HEM401 3.0 25.6 1.0
C1A A:HEM401 3.0 26.3 1.0
C1D A:HEM401 3.0 24.4 1.0
C4A A:HEM401 3.0 25.0 1.0
C1B A:HEM401 3.0 24.6 1.0
C4B A:HEM401 3.0 23.6 1.0
CD2 A:HIS225 3.1 24.1 1.0
C1C A:HEM401 3.1 22.9 1.0
C4C A:HEM401 3.1 22.5 1.0
CE1 A:HIS225 3.1 22.3 1.0
CHB A:HEM401 3.4 23.0 1.0
CHA A:HEM401 3.4 24.0 1.0
CHC A:HEM401 3.4 22.8 1.0
CHD A:HEM401 3.5 23.2 1.0
CG A:HIS225 4.2 23.0 1.0
C2A A:HEM401 4.2 24.2 1.0
C3A A:HEM401 4.2 25.1 1.0
ND1 A:HIS225 4.2 23.6 1.0
NH1 A:ARG243 4.2 25.2 1.0
C3D A:HEM401 4.3 26.0 1.0
C2D A:HEM401 4.3 26.9 1.0
C2B A:HEM401 4.3 23.4 1.0
C3B A:HEM401 4.3 25.4 1.0
CD A:ARG243 4.3 24.4 1.0
C2C A:HEM401 4.3 23.6 1.0
C3C A:HEM401 4.3 23.1 1.0
ND2 A:ASN245 4.5 34.2 1.0
CZ A:ARG243 4.8 23.9 1.0
NE A:ARG243 4.8 24.4 1.0

Iron binding site 2 out of 6 in 6yrc

Go back to Iron Binding Sites List in 6yrc
Iron binding site 2 out of 6 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

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

b:27.0
occ:1.00
FE B:HEM401 0.0 27.0 1.0
ND B:HEM401 1.9 25.2 1.0
NA B:HEM401 2.0 23.3 1.0
NC B:HEM401 2.1 24.4 1.0
NB B:HEM401 2.1 26.2 1.0
NE2 B:HIS225 2.1 23.2 1.0
C4D B:HEM401 3.0 25.3 1.0
C1D B:HEM401 3.0 25.3 1.0
C1A B:HEM401 3.0 26.0 1.0
C4B B:HEM401 3.0 24.8 1.0
CD2 B:HIS225 3.0 25.7 1.0
C4C B:HEM401 3.1 25.2 1.0
C1B B:HEM401 3.1 27.0 1.0
C4A B:HEM401 3.1 25.5 1.0
C1C B:HEM401 3.1 24.9 1.0
CE1 B:HIS225 3.1 24.1 1.0
CHA B:HEM401 3.4 26.6 1.0
CHC B:HEM401 3.4 23.8 1.0
CHD B:HEM401 3.4 25.4 1.0
CHB B:HEM401 3.5 25.9 1.0
NH1 B:ARG243 4.0 32.3 1.0
CG B:HIS225 4.2 23.7 1.0
ND1 B:HIS225 4.2 23.8 1.0
ND2 B:ASN245 4.2 29.2 1.0
C2D B:HEM401 4.2 26.3 1.0
C3D B:HEM401 4.2 27.1 1.0
C2A B:HEM401 4.2 24.3 1.0
C3A B:HEM401 4.3 25.9 1.0
C3C B:HEM401 4.3 23.8 1.0
C2C B:HEM401 4.3 25.2 1.0
C3B B:HEM401 4.3 23.2 1.0
C2B B:HEM401 4.3 26.2 1.0
CD B:ARG243 4.3 26.8 1.0
CZ B:ARG243 4.7 27.9 1.0
NE B:ARG243 4.8 31.3 1.0

Iron binding site 3 out of 6 in 6yrc

Go back to Iron Binding Sites List in 6yrc
Iron binding site 3 out of 6 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

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

b:24.8
occ:1.00
FE C:HEM401 0.0 24.8 1.0
ND C:HEM401 1.9 24.1 1.0
NA C:HEM401 2.0 25.3 1.0
NB C:HEM401 2.1 23.7 1.0
NC C:HEM401 2.1 23.4 1.0
NE2 C:HIS225 2.1 23.3 1.0
C4D C:HEM401 3.0 23.2 1.0
C1D C:HEM401 3.0 23.8 1.0
C1A C:HEM401 3.0 25.1 1.0
C4B C:HEM401 3.0 25.0 1.0
CD2 C:HIS225 3.0 25.1 1.0
C4A C:HEM401 3.0 26.3 1.0
C4C C:HEM401 3.1 24.3 1.0
C1B C:HEM401 3.1 25.6 1.0
C1C C:HEM401 3.1 23.6 1.0
CE1 C:HIS225 3.1 25.4 1.0
CHA C:HEM401 3.4 23.4 1.0
CHC C:HEM401 3.4 22.9 1.0
CHD C:HEM401 3.5 22.7 1.0
CHB C:HEM401 3.5 24.5 1.0
C2A C:HEM401 4.2 25.1 1.0
CG C:HIS225 4.2 25.4 1.0
ND1 C:HIS225 4.2 22.7 1.0
C3A C:HEM401 4.2 25.7 1.0
NH1 C:ARG243 4.2 33.1 1.0
C3D C:HEM401 4.2 25.6 1.0
C2D C:HEM401 4.2 24.2 1.0
C3C C:HEM401 4.3 24.9 1.0
C3B C:HEM401 4.3 25.2 1.0
C2C C:HEM401 4.3 22.2 1.0
C2B C:HEM401 4.3 25.1 1.0
CD C:ARG243 4.4 28.9 1.0
ND2 C:ASN245 4.4 35.7 1.0
CZ C:ARG243 4.8 30.6 1.0
NE C:ARG243 4.9 30.7 1.0
CG2 C:THR229 5.0 26.6 1.0

Iron binding site 4 out of 6 in 6yrc

Go back to Iron Binding Sites List in 6yrc
Iron binding site 4 out of 6 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

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

b:23.3
occ:1.00
FE D:HEM401 0.0 23.3 1.0
ND D:HEM401 1.9 22.5 1.0
NA D:HEM401 2.0 23.7 1.0
NB D:HEM401 2.1 25.0 1.0
NC D:HEM401 2.1 23.0 1.0
NE2 D:HIS225 2.1 23.5 1.0
C4D D:HEM401 2.9 23.5 1.0
C1D D:HEM401 3.0 24.0 1.0
C1A D:HEM401 3.0 21.8 1.0
C4B D:HEM401 3.0 26.9 1.0
C4A D:HEM401 3.0 23.1 1.0
CD2 D:HIS225 3.0 23.4 1.0
C1B D:HEM401 3.1 26.0 1.0
C4C D:HEM401 3.1 24.4 1.0
CE1 D:HIS225 3.1 25.2 1.0
C1C D:HEM401 3.1 23.4 1.0
CHA D:HEM401 3.4 22.7 1.0
CHC D:HEM401 3.4 25.0 1.0
CHB D:HEM401 3.5 26.5 1.0
CHD D:HEM401 3.5 23.9 1.0
NH1 D:ARG243 4.1 27.3 1.0
CG D:HIS225 4.2 25.6 1.0
ND1 D:HIS225 4.2 23.2 1.0
C3D D:HEM401 4.2 23.2 1.0
C2A D:HEM401 4.2 23.5 1.0
C3A D:HEM401 4.2 25.1 1.0
C2D D:HEM401 4.2 23.0 1.0
C2C D:HEM401 4.3 23.4 1.0
C3C D:HEM401 4.3 22.8 1.0
C3B D:HEM401 4.3 24.6 1.0
C2B D:HEM401 4.3 27.2 1.0
ND2 D:ASN245 4.3 34.3 1.0
CD D:ARG243 4.4 28.9 1.0
CZ D:ARG243 4.7 25.5 1.0
NE D:ARG243 4.8 28.5 1.0

Iron binding site 5 out of 6 in 6yrc

Go back to Iron Binding Sites List in 6yrc
Iron binding site 5 out of 6 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

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

b:26.3
occ:1.00
FE E:HEM401 0.0 26.3 1.0
ND E:HEM401 1.9 25.0 1.0
NE2 E:HIS225 2.0 27.7 1.0
NA E:HEM401 2.0 23.7 1.0
NB E:HEM401 2.1 24.8 1.0
NC E:HEM401 2.1 23.9 1.0
C4D E:HEM401 2.9 25.2 1.0
C1D E:HEM401 3.0 25.8 1.0
C1A E:HEM401 3.0 25.4 1.0
C4B E:HEM401 3.0 25.1 1.0
CD2 E:HIS225 3.0 26.9 1.0
CE1 E:HIS225 3.0 29.3 1.0
C4A E:HEM401 3.1 26.5 1.0
C1B E:HEM401 3.1 26.2 1.0
C4C E:HEM401 3.1 24.2 1.0
C1C E:HEM401 3.1 23.1 1.0
CHA E:HEM401 3.3 24.4 1.0
CHD E:HEM401 3.4 26.3 1.0
CHC E:HEM401 3.4 25.7 1.0
CHB E:HEM401 3.5 24.5 1.0
NH1 E:ARG243 4.1 32.3 1.0
ND1 E:HIS225 4.1 26.3 1.0
CG E:HIS225 4.1 27.3 1.0
C3D E:HEM401 4.2 28.0 1.0
C2D E:HEM401 4.2 25.9 1.0
ND2 E:ASN245 4.2 35.0 1.0
C2A E:HEM401 4.2 27.1 1.0
C3A E:HEM401 4.3 28.3 1.0
C3B E:HEM401 4.3 27.0 1.0
CD E:ARG243 4.3 28.2 1.0
C2B E:HEM401 4.3 25.8 1.0
C2C E:HEM401 4.3 24.1 1.0
C3C E:HEM401 4.3 22.9 1.0
CZ E:ARG243 4.6 28.8 1.0
NE E:ARG243 4.7 30.5 1.0

Iron binding site 6 out of 6 in 6yrc

Go back to Iron Binding Sites List in 6yrc
Iron binding site 6 out of 6 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

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

b:25.3
occ:1.00
FE F:HEM401 0.0 25.3 1.0
ND F:HEM401 1.9 25.0 1.0
NA F:HEM401 2.0 24.9 1.0
NB F:HEM401 2.1 24.3 1.0
NE2 F:HIS225 2.1 22.3 1.0
NC F:HEM401 2.1 23.9 1.0
C4D F:HEM401 2.9 26.2 1.0
C1D F:HEM401 3.0 24.7 1.0
C1A F:HEM401 3.0 25.7 1.0
C4B F:HEM401 3.0 23.9 1.0
CD2 F:HIS225 3.1 22.7 1.0
C1B F:HEM401 3.1 25.3 1.0
CE1 F:HIS225 3.1 24.4 1.0
C4A F:HEM401 3.1 24.7 1.0
C4C F:HEM401 3.1 25.2 1.0
C1C F:HEM401 3.1 24.1 1.0
CHA F:HEM401 3.4 26.0 1.0
CHC F:HEM401 3.4 22.0 1.0
CHD F:HEM401 3.4 23.9 1.0
CHB F:HEM401 3.5 22.9 1.0
NH1 F:ARG243 4.1 27.3 1.0
ND1 F:HIS225 4.2 22.0 1.0
CG F:HIS225 4.2 23.5 1.0
C2A F:HEM401 4.2 23.8 1.0
C2D F:HEM401 4.2 24.2 1.0
C3D F:HEM401 4.2 24.7 1.0
C3A F:HEM401 4.2 24.4 1.0
C3B F:HEM401 4.3 23.2 1.0
C2B F:HEM401 4.3 23.0 1.0
C2C F:HEM401 4.3 24.9 1.0
C3C F:HEM401 4.3 24.2 1.0
ND2 F:ASN245 4.4 31.6 1.0
CD F:ARG243 4.4 27.1 1.0
CZ F:ARG243 4.7 27.8 1.0
NE F:ARG243 4.8 27.8 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 6 16:36:40 2025

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