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Iron in PDB 7m1j: Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol

Protein crystallography data

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol, PDB code: 7m1j was solved by R.A.Ghiladi, V.S.De Serrano, T.Malewschik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.40 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.756, 66.594, 68.283, 90, 90, 90
R / Rfree (%) 14.6 / 20.6

Other elements in 7m1j:

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol (pdb code 7m1j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol, PDB code: 7m1j:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 7m1j

Go back to Iron Binding Sites List in 7m1j
Iron binding site 1 out of 2 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:34.7
occ:1.00
FE A:HEM201 0.0 34.7 1.0
ND A:HEM201 1.9 36.3 1.0
NA A:HEM201 2.0 33.8 1.0
NE2 A:HIS89 2.0 38.2 1.0
NB A:HEM201 2.1 77.8 1.0
NC A:HEM201 2.1 36.0 1.0
NE2 A:HIS55 2.2 41.2 0.7
C4D A:HEM201 2.8 37.8 1.0
C1D A:HEM201 2.9 38.0 1.0
C1A A:HEM201 3.0 35.8 1.0
CD2 A:HIS89 3.0 52.3 1.0
C1B A:HEM201 3.1 38.7 1.0
C4C A:HEM201 3.1 37.0 1.0
CE1 A:HIS89 3.1 48.0 1.0
C4A A:HEM201 3.1 33.3 1.0
C4B A:HEM201 3.1 35.6 1.0
CD2 A:HIS55 3.1 23.2 0.7
CE1 A:HIS55 3.2 26.0 0.7
C1C A:HEM201 3.2 44.5 1.0
CHA A:HEM201 3.3 39.6 1.0
CHD A:HEM201 3.4 38.1 1.0
CHB A:HEM201 3.5 35.3 1.0
CHC A:HEM201 3.6 39.3 1.0
C3D A:HEM201 4.1 35.3 1.0
C2D A:HEM201 4.1 37.7 1.0
CG A:HIS89 4.1 40.8 1.0
ND1 A:HIS89 4.2 46.0 1.0
C2A A:HEM201 4.2 49.9 1.0
ND1 A:HIS55 4.3 20.5 0.7
CG A:HIS55 4.3 21.5 0.7
C3A A:HEM201 4.3 43.9 1.0
C2B A:HEM201 4.3 36.4 1.0
C3C A:HEM201 4.3 38.5 1.0
C2C A:HEM201 4.4 42.0 1.0
CG2 A:VAL59 4.4 21.9 1.0
C3B A:HEM201 4.4 37.4 1.0
CD1 A:LEU92 4.9 48.8 1.0

Iron binding site 2 out of 2 in 7m1j

Go back to Iron Binding Sites List in 7m1j
Iron binding site 2 out of 2 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:20.2
occ:1.00
FE B:HEM201 0.0 20.2 1.0
ND B:HEM201 2.0 21.9 1.0
NA B:HEM201 2.0 19.7 1.0
NB B:HEM201 2.1 15.9 1.0
NC B:HEM201 2.1 21.0 1.0
NE2 B:HIS89 2.1 20.5 1.0
C B:94N202 2.3 25.3 0.7
C1 B:94N202 2.8 44.7 0.7
C1D B:HEM201 3.0 20.8 1.0
C1B B:HEM201 3.1 16.4 1.0
C4B B:HEM201 3.1 16.8 1.0
C1A B:HEM201 3.1 21.2 1.0
C4C B:HEM201 3.1 21.2 1.0
C4A B:HEM201 3.1 18.0 1.0
C4D B:HEM201 3.1 21.4 1.0
C1C B:HEM201 3.1 19.4 1.0
CE1 B:HIS89 3.1 27.5 1.0
CD2 B:HIS89 3.2 23.4 1.0
CHD B:HEM201 3.4 20.0 1.0
C5 B:94N202 3.4 41.1 0.7
CHB B:HEM201 3.5 17.1 1.0
CHC B:HEM201 3.5 17.9 1.0
CHA B:HEM201 3.6 21.4 1.0
C2 B:94N202 4.2 56.7 0.7
ND1 B:HIS89 4.2 23.2 1.0
C2D B:HEM201 4.3 24.3 1.0
C2A B:HEM201 4.3 18.4 1.0
C3A B:HEM201 4.3 18.1 1.0
C3C B:HEM201 4.3 20.2 1.0
C2B B:HEM201 4.3 17.4 1.0
CG B:HIS89 4.3 23.4 1.0
C3D B:HEM201 4.3 25.2 1.0
C2C B:HEM201 4.3 20.2 1.0
C3B B:HEM201 4.3 18.2 1.0
CG2 B:VAL59 4.4 18.7 1.0
C4 B:94N202 4.6 51.8 0.7
CG1 B:VAL59 4.7 18.2 1.0
CE B:MET86 4.9 20.2 1.0
C3 B:94N202 5.0 53.6 0.7

Reference:

T.Malewschik, L.M.Carey, V.De Serrano, R.A.Ghiladi. Bridging the Functional Gap Between Reactivity and Inhibition in Dehaloperoxidase B From Amphitrite Ornata: Mechanistic and Structural Studies with 2,4- and 2,6-Dihalophenols. J.Inorg.Biochem. V. 236 11944 2022.
ISSN: ISSN 0162-0134
PubMed: 35969974
DOI: 10.1016/J.JINORGBIO.2022.111944
Page generated: Thu Aug 8 08:08:38 2024

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