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Iron in PDB 6i8j: Dye Type Peroxidase Aa From Streptomyces Lividans: 131.2 Kgy Structure

Protein crystallography data

The structure of Dye Type Peroxidase Aa From Streptomyces Lividans: 131.2 Kgy Structure, PDB code: 6i8j was solved by A.Ebrahim, T.Moreno-Chicano, J.A.R.Worrall, R.W.Strange, D.Axford, D.A.Sherrell, M.Appleby, R.L.Owen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.61 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.989, 68.288, 74.863, 90.00, 105.76, 90.00
R / Rfree (%) 16.7 / 21.2

Iron Binding Sites:

The binding sites of Iron atom in the Dye Type Peroxidase Aa From Streptomyces Lividans: 131.2 Kgy Structure (pdb code 6i8j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Dye Type Peroxidase Aa From Streptomyces Lividans: 131.2 Kgy Structure, PDB code: 6i8j:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6i8j

Go back to Iron Binding Sites List in 6i8j
Iron binding site 1 out of 2 in the Dye Type Peroxidase Aa From Streptomyces Lividans: 131.2 Kgy 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 Aa From Streptomyces Lividans: 131.2 Kgy Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:19.2
occ:1.00
FE A:HEM501 0.0 19.2 1.0
NC A:HEM501 2.0 20.8 1.0
NA A:HEM501 2.0 19.6 1.0
NB A:HEM501 2.0 16.9 1.0
ND A:HEM501 2.1 21.2 1.0
NE2 A:HIS326 2.3 17.8 1.0
O A:HOH643 2.7 24.9 1.0
C4A A:HEM501 3.0 20.8 1.0
C4C A:HEM501 3.0 21.4 1.0
C1B A:HEM501 3.0 21.9 1.0
C1C A:HEM501 3.0 21.5 1.0
C4B A:HEM501 3.1 18.2 1.0
C1A A:HEM501 3.1 20.2 1.0
C1D A:HEM501 3.1 20.2 1.0
C4D A:HEM501 3.1 19.3 1.0
CD2 A:HIS326 3.2 18.7 1.0
CE1 A:HIS326 3.2 19.3 1.0
CHB A:HEM501 3.4 22.2 1.0
CHD A:HEM501 3.4 22.1 1.0
CHC A:HEM501 3.4 17.5 1.0
CHA A:HEM501 3.5 20.5 1.0
O A:HOH706 4.1 34.3 1.0
C3C A:HEM501 4.2 23.1 1.0
NH1 A:ARG342 4.2 23.3 1.0
C3A A:HEM501 4.2 20.6 1.0
C2C A:HEM501 4.2 23.4 1.0
C2B A:HEM501 4.3 19.6 1.0
C2A A:HEM501 4.3 17.6 1.0
C3B A:HEM501 4.3 20.9 1.0
C2D A:HEM501 4.3 25.6 1.0
ND1 A:HIS326 4.3 18.6 1.0
CG A:HIS326 4.3 20.5 1.0
C3D A:HEM501 4.3 21.0 1.0
CD A:ARG342 4.8 25.9 1.0
OD1 A:ASP239 4.8 23.3 1.0
CZ A:ARG342 5.0 25.3 1.0

Iron binding site 2 out of 2 in 6i8j

Go back to Iron Binding Sites List in 6i8j
Iron binding site 2 out of 2 in the Dye Type Peroxidase Aa From Streptomyces Lividans: 131.2 Kgy 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 Aa From Streptomyces Lividans: 131.2 Kgy Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:19.7
occ:1.00
FE B:HEM501 0.0 19.7 1.0
NC B:HEM501 2.0 20.4 1.0
NB B:HEM501 2.0 18.2 1.0
ND B:HEM501 2.0 19.7 1.0
NA B:HEM501 2.1 20.6 1.0
NE2 B:HIS326 2.3 20.2 1.0
O B:HOH691 2.9 30.2 1.0
C4C B:HEM501 3.0 22.1 1.0
C1D B:HEM501 3.0 23.3 1.0
C1B B:HEM501 3.0 19.7 1.0
C1C B:HEM501 3.0 21.0 1.0
C4A B:HEM501 3.0 18.6 1.0
C4B B:HEM501 3.1 18.8 1.0
C1A B:HEM501 3.1 21.3 1.0
C4D B:HEM501 3.1 22.4 1.0
CE1 B:HIS326 3.2 26.8 1.0
CD2 B:HIS326 3.2 22.0 1.0
CHD B:HEM501 3.4 19.9 1.0
CHB B:HEM501 3.4 23.0 1.0
CHC B:HEM501 3.4 23.3 1.0
CHA B:HEM501 3.5 23.7 1.0
C3C B:HEM501 4.2 18.4 1.0
C2C B:HEM501 4.2 19.4 1.0
C2B B:HEM501 4.3 18.8 1.0
C3A B:HEM501 4.3 23.6 1.0
C2D B:HEM501 4.3 23.3 1.0
C3B B:HEM501 4.3 17.7 1.0
NH1 B:ARG342 4.3 22.6 1.0
C2A B:HEM501 4.3 23.2 1.0
C3D B:HEM501 4.3 21.1 1.0
ND1 B:HIS326 4.3 24.4 1.0
CG B:HIS326 4.4 21.5 1.0
CD B:ARG342 4.8 22.7 1.0
CZ B:ARG342 5.0 23.6 1.0

Reference:

A.Ebrahim, T.Moreno-Chicano, M.V.Appleby, A.K.Chaplin, J.H.Beale, D.A.Sherrell, H.M.E.Duyvesteyn, S.Owada, K.Tono, H.Sugimoto, R.W.Strange, J.A.R.Worrall, D.Axford, R.L.Owen, M.A.Hough. Dose-Resolved Serial Synchrotron and Xfel Structures of Radiation-Sensitive Metalloproteins. Iucrj V. 6 543 2019.
ISSN: ESSN 2052-2525
PubMed: 31316799
DOI: 10.1107/S2052252519003956
Page generated: Tue Aug 6 22:14:03 2024

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