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Iron in PDB 8doh: Dehaloperoxidase B in Complex with Bisphenol F

Protein crystallography data

The structure of Dehaloperoxidase B in Complex with Bisphenol F, PDB code: 8doh was solved by V.S.De Serrano, D.Yun, R.Ghiladi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.30 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.672, 67.281, 67.704, 90, 90, 90
R / Rfree (%) 17 / 22

Iron Binding Sites:

The binding sites of Iron atom in the Dehaloperoxidase B in Complex with Bisphenol F (pdb code 8doh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Dehaloperoxidase B in Complex with Bisphenol F, PDB code: 8doh:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 8doh

Go back to Iron Binding Sites List in 8doh
Iron binding site 1 out of 2 in the Dehaloperoxidase B in Complex with Bisphenol F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dehaloperoxidase B in Complex with Bisphenol F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:19.9
occ:1.00
FE A:HEM201 0.0 19.9 1.0
NA A:HEM201 1.9 19.8 1.0
ND A:HEM201 2.0 20.0 1.0
NC A:HEM201 2.0 19.5 1.0
NB A:HEM201 2.1 17.2 1.0
NE2 A:HIS89 2.2 23.4 1.0
C1D A:HEM201 2.9 22.2 1.0
C4D A:HEM201 3.0 21.1 1.0
C4C A:HEM201 3.0 21.2 1.0
C1A A:HEM201 3.0 18.5 1.0
C4A A:HEM201 3.0 18.2 1.0
C4B A:HEM201 3.0 17.3 1.0
C1C A:HEM201 3.1 20.4 1.0
C1B A:HEM201 3.1 16.4 1.0
CE1 A:HIS89 3.1 23.6 1.0
CD2 A:HIS89 3.2 25.3 1.0
CHD A:HEM201 3.4 22.2 1.0
C7 A:T0U202 3.4 57.7 0.5
CHC A:HEM201 3.4 18.4 1.0
CHB A:HEM201 3.4 17.8 1.0
CHA A:HEM201 3.5 18.6 1.0
C3C A:HEM201 4.2 20.9 1.0
C2A A:HEM201 4.2 19.9 1.0
C2C A:HEM201 4.2 21.5 1.0
C2D A:HEM201 4.2 21.9 1.0
C3A A:HEM201 4.2 18.1 1.0
C3D A:HEM201 4.2 22.2 1.0
C13 A:T0U202 4.2 15.0 0.4
ND1 A:HIS89 4.3 23.8 1.0
C2B A:HEM201 4.3 17.4 1.0
CG A:HIS89 4.3 25.4 1.0
C3B A:HEM201 4.3 16.4 1.0
C6 A:T0U202 4.4 62.7 0.5
CG2 A:VAL59 4.4 14.6 1.0
C8 A:T0U202 4.5 60.0 0.5
C7 A:T0U202 4.7 14.3 0.4
C13 A:T0U202 4.7 60.4 0.5
CG1 A:VAL59 4.8 13.4 1.0
C1 A:T0U202 4.9 63.5 0.5
CE A:MET86 4.9 29.6 1.0
C8 A:T0U202 5.0 14.4 0.4

Iron binding site 2 out of 2 in 8doh

Go back to Iron Binding Sites List in 8doh
Iron binding site 2 out of 2 in the Dehaloperoxidase B in Complex with Bisphenol F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dehaloperoxidase B in Complex with Bisphenol F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:16.6
occ:1.00
FE B:HEM201 0.0 16.6 1.0
ND B:HEM201 1.9 18.0 1.0
NA B:HEM201 1.9 15.4 1.0
NC B:HEM201 2.1 16.7 1.0
NB B:HEM201 2.1 14.3 1.0
NE2 B:HIS89 2.1 18.1 1.0
O B:HOH347 2.4 9.3 0.4
C1D B:HEM201 2.9 16.6 1.0
C4D B:HEM201 3.0 17.4 1.0
C4A B:HEM201 3.0 13.8 1.0
C1B B:HEM201 3.0 13.2 1.0
C1A B:HEM201 3.0 15.9 1.0
C4B B:HEM201 3.0 14.2 1.0
CE1 B:HIS89 3.1 18.3 1.0
C4C B:HEM201 3.1 16.9 1.0
C1C B:HEM201 3.1 15.3 1.0
CD2 B:HIS89 3.1 18.9 1.0
CHB B:HEM201 3.4 14.2 1.0
CHD B:HEM201 3.4 17.1 1.0
CHA B:HEM201 3.5 15.6 1.0
CHC B:HEM201 3.5 14.4 1.0
C7 B:T0U202 3.6 39.0 0.6
C13 B:T0U202 3.9 52.7 0.6
C3D B:HEM201 4.2 19.9 1.0
C2D B:HEM201 4.2 19.9 1.0
ND1 B:HIS89 4.2 18.4 1.0
C2A B:HEM201 4.2 16.0 1.0
C3A B:HEM201 4.2 15.5 1.0
C2B B:HEM201 4.3 12.8 1.0
C8 B:T0U202 4.3 49.0 0.6
CG B:HIS89 4.3 18.6 1.0
C3B B:HEM201 4.3 13.5 1.0
C1 B:T0U202 4.3 38.6 0.6
C2C B:HEM201 4.3 15.6 1.0
C3C B:HEM201 4.3 17.5 1.0
C6 B:T0U202 4.4 37.3 0.6
CG2 B:VAL59 4.4 14.0 1.0
CG1 B:VAL59 4.8 14.3 1.0
CE B:MET86 4.9 23.4 1.0
NE2 B:HIS55 4.9 19.7 0.4

Reference:

D.Yun, V.De Serrano, R.A.Ghiladi. Oxidation of Bisphenol A (Bpa) and Related Compounds By the Multifunctional Catalytic Globin Dehaloperoxidase. J.Inorg.Biochem. V. 238 12020 2023.
ISSN: ISSN 0162-0134
PubMed: 36272837
DOI: 10.1016/J.JINORGBIO.2022.112020
Page generated: Sat Aug 10 00:14:44 2024

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