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Iron in PDB 6i8e: Dye Type Peroxidase Aa From Streptomyces Lividans: 65.6 Kgy Structure

Protein crystallography data

The structure of Dye Type Peroxidase Aa From Streptomyces Lividans: 65.6 Kgy Structure, PDB code: 6i8e 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 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.961, 68.298, 74.787, 90.00, 105.69, 90.00
R / Rfree (%) 16.6 / 21.1

Iron Binding Sites:

The binding sites of Iron atom in the Dye Type Peroxidase Aa From Streptomyces Lividans: 65.6 Kgy Structure (pdb code 6i8e). 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: 65.6 Kgy Structure, PDB code: 6i8e:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6i8e

Go back to Iron Binding Sites List in 6i8e
Iron binding site 1 out of 2 in the Dye Type Peroxidase Aa From Streptomyces Lividans: 65.6 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: 65.6 Kgy Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:16.4
occ:1.00
FE A:HEM501 0.0 16.4 1.0
NB A:HEM501 2.0 16.1 1.0
NC A:HEM501 2.0 16.3 1.0
NA A:HEM501 2.1 17.1 1.0
ND A:HEM501 2.1 16.9 1.0
NE2 A:HIS326 2.2 15.9 1.0
O A:HOH692 2.7 22.6 1.0
C1B A:HEM501 3.0 18.6 1.0
C1C A:HEM501 3.0 17.7 1.0
C4C A:HEM501 3.0 17.8 1.0
C4B A:HEM501 3.0 15.1 1.0
C4A A:HEM501 3.1 15.2 1.0
C1D A:HEM501 3.1 16.0 1.0
C1A A:HEM501 3.1 15.2 1.0
C4D A:HEM501 3.1 16.9 1.0
CD2 A:HIS326 3.2 15.7 1.0
CE1 A:HIS326 3.2 17.6 1.0
CHB A:HEM501 3.4 17.9 1.0
CHD A:HEM501 3.4 20.3 1.0
CHC A:HEM501 3.4 17.6 1.0
CHA A:HEM501 3.5 15.2 1.0
C2B A:HEM501 4.2 14.7 1.0
C2C A:HEM501 4.2 22.2 1.0
C3C A:HEM501 4.2 19.2 1.0
C3B A:HEM501 4.3 14.1 1.0
C3A A:HEM501 4.3 17.2 1.0
C2D A:HEM501 4.3 17.2 1.0
C2A A:HEM501 4.3 13.7 1.0
NH1 A:ARG342 4.3 18.2 1.0
C3D A:HEM501 4.3 17.2 1.0
ND1 A:HIS326 4.3 15.7 1.0
CG A:HIS326 4.3 17.3 1.0
O A:HOH632 4.4 29.0 1.0
CD A:ARG342 4.8 19.9 1.0
OD1 A:ASP239 4.8 20.2 1.0
CZ A:ARG342 5.0 16.3 1.0

Iron binding site 2 out of 2 in 6i8e

Go back to Iron Binding Sites List in 6i8e
Iron binding site 2 out of 2 in the Dye Type Peroxidase Aa From Streptomyces Lividans: 65.6 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: 65.6 Kgy Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:17.0
occ:1.00
FE B:HEM501 0.0 17.0 1.0
NB B:HEM501 2.0 18.6 1.0
NC B:HEM501 2.0 14.2 1.0
NA B:HEM501 2.1 16.3 1.0
ND B:HEM501 2.1 16.5 1.0
NE2 B:HIS326 2.2 15.3 1.0
C1B B:HEM501 3.0 17.0 1.0
C4A B:HEM501 3.0 16.2 1.0
C4C B:HEM501 3.0 16.1 1.0
C4B B:HEM501 3.0 16.2 1.0
C1C B:HEM501 3.0 17.4 1.0
C1D B:HEM501 3.1 17.2 1.0
C1A B:HEM501 3.1 18.4 1.0
O B:HOH755 3.1 27.5 1.0
C4D B:HEM501 3.1 16.4 1.0
CE1 B:HIS326 3.1 18.1 1.0
CD2 B:HIS326 3.3 16.4 1.0
CHB B:HEM501 3.4 19.1 1.0
CHD B:HEM501 3.4 15.7 1.0
CHC B:HEM501 3.4 17.7 1.0
CHA B:HEM501 3.5 18.7 1.0
NH1 B:ARG342 4.2 21.6 1.0
C2B B:HEM501 4.2 17.2 1.0
C3B B:HEM501 4.3 16.7 1.0
C3A B:HEM501 4.3 21.1 1.0
C2C B:HEM501 4.3 15.3 1.0
C3C B:HEM501 4.3 16.7 1.0
C2D B:HEM501 4.3 19.3 1.0
ND1 B:HIS326 4.3 19.0 1.0
C2A B:HEM501 4.3 19.1 1.0
C3D B:HEM501 4.3 15.5 1.0
CG B:HIS326 4.4 19.1 1.0
CD B:ARG342 4.9 19.1 1.0
CZ B:ARG342 5.0 19.8 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: Sun Dec 13 16:33:55 2020

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