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Iron in PDB 6vds: Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol

Protein crystallography data

The structure of Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol, PDB code: 6vds was solved by R.A.Ghiladi, V.S.De Serrano, A.Mcguire, T.Malewschik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.89 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.562, 67.491, 67.951, 90, 90, 90
R / Rfree (%) 21.5 / 25.6

Other elements in 6vds:

The structure of Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol 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 Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol (pdb code 6vds). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol, PDB code: 6vds:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 6vds

Go back to Iron Binding Sites List in 6vds
Iron binding site 1 out of 3 in the Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol


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 Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:40.1
occ:1.00
FE A:FDE201 0.0 40.1 1.0
NA A:FDE201 2.0 41.5 1.0
NE2 A:HIS89 2.1 47.0 1.0
NC A:FDE201 2.1 41.9 1.0
NB A:FDE201 2.1 40.5 1.0
ND A:FDE201 2.1 41.2 1.0
NE2 A:HIS55 2.1 33.0 1.0
CD2 A:HIS89 3.0 47.1 1.0
C1A A:FDE201 3.1 40.3 1.0
C1C A:FDE201 3.1 42.6 1.0
CE1 A:HIS55 3.1 32.2 1.0
C4C A:FDE201 3.1 44.4 1.0
C4A A:FDE201 3.1 40.1 1.0
CE1 A:HIS89 3.1 46.0 1.0
C4B A:FDE201 3.1 40.6 1.0
C4D A:FDE201 3.1 43.3 1.0
C1B A:FDE201 3.1 39.4 1.0
C1D A:FDE201 3.1 44.0 1.0
CD2 A:HIS55 3.2 34.6 1.0
CHA A:FDE201 3.5 40.8 1.0
CHD A:FDE201 3.5 42.6 1.0
CHC A:FDE201 3.5 41.6 1.0
CHB A:FDE201 3.5 40.5 1.0
CG A:HIS89 4.2 46.2 1.0
ND1 A:HIS89 4.2 44.5 1.0
ND1 A:HIS55 4.2 31.5 1.0
CG A:HIS55 4.3 31.8 1.0
C2C A:FDE201 4.3 43.9 1.0
C3C A:FDE201 4.3 41.4 1.0
C2A A:FDE201 4.4 43.8 1.0
C2B A:FDE201 4.4 39.6 1.0
C3B A:FDE201 4.4 40.7 1.0
C3A A:FDE201 4.4 43.2 1.0
C3D A:FDE201 4.4 44.8 1.0
C2D A:FDE201 4.5 43.1 1.0

Iron binding site 2 out of 3 in 6vds

Go back to Iron Binding Sites List in 6vds
Iron binding site 2 out of 3 in the Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol


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 Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:64.1
occ:0.50
FE B:FDE201 0.0 64.1 0.5
FE B:FDE201 0.3 34.4 0.5
ND B:FDE201 1.9 35.4 0.5
NA B:FDE201 2.0 64.6 0.5
NA B:FDE201 2.0 34.5 0.5
NC B:FDE201 2.1 32.6 0.5
NC B:FDE201 2.1 61.9 0.5
NB B:FDE201 2.1 62.5 0.5
ND B:FDE201 2.1 62.8 0.5
NE2 B:HIS55 2.2 33.2 1.0
NE2 B:HIS89 2.2 52.3 1.0
NB B:FDE201 2.4 33.2 0.5
C1D B:FDE201 2.9 35.0 0.5
C4D B:FDE201 2.9 35.9 0.5
C4C B:FDE201 3.0 32.5 0.5
C1A B:FDE201 3.0 35.3 0.5
C1A B:FDE201 3.0 64.4 0.5
C4A B:FDE201 3.1 64.5 0.5
CD2 B:HIS89 3.1 52.9 1.0
C4D B:FDE201 3.1 62.1 0.5
C1C B:FDE201 3.1 60.7 0.5
C4C B:FDE201 3.1 60.8 0.5
C1B B:FDE201 3.1 63.1 0.5
C1D B:FDE201 3.1 61.0 0.5
C4B B:FDE201 3.1 61.8 0.5
CE1 B:HIS55 3.1 33.1 1.0
CD2 B:HIS55 3.2 33.9 1.0
C1C B:FDE201 3.2 32.0 0.5
C4A B:FDE201 3.2 33.8 0.5
CE1 B:HIS89 3.3 55.2 1.0
CHD B:FDE201 3.3 33.7 0.5
CHA B:FDE201 3.4 36.3 0.5
C4B B:FDE201 3.4 31.8 0.5
C1B B:FDE201 3.4 32.2 0.5
CHA B:FDE201 3.5 63.9 0.5
CHD B:FDE201 3.5 60.6 0.5
CHB B:FDE201 3.5 64.0 0.5
CHC B:FDE201 3.5 61.5 0.5
CHC B:FDE201 3.7 32.6 0.5
CHB B:FDE201 3.7 32.6 0.5
C2D B:FDE201 4.2 36.6 0.5
ND1 B:HIS55 4.2 31.9 1.0
C3D B:FDE201 4.2 37.0 0.5
CG B:HIS89 4.3 52.9 1.0
CG B:HIS55 4.3 32.3 1.0
C2A B:FDE201 4.3 64.8 0.5
C3C B:FDE201 4.3 32.9 0.5
C3A B:FDE201 4.3 65.8 0.5
C2A B:FDE201 4.3 36.7 0.5
ND1 B:HIS89 4.3 53.5 1.0
C2C B:FDE201 4.4 61.1 0.5
C3C B:FDE201 4.4 59.4 0.5
C2C B:FDE201 4.4 32.1 0.5
C2B B:FDE201 4.4 63.7 0.5
C3B B:FDE201 4.4 62.4 0.5
C3A B:FDE201 4.4 34.4 0.5
C3D B:FDE201 4.5 61.9 0.5
C2D B:FDE201 4.5 60.7 0.5
C2B B:FDE201 4.7 30.7 0.5
C3B B:FDE201 4.7 32.1 0.5

Iron binding site 3 out of 3 in 6vds

Go back to Iron Binding Sites List in 6vds
Iron binding site 3 out of 3 in the Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-Bromo-Ortho-Cresol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:34.4
occ:0.50
FE B:FDE201 0.0 34.4 0.5
FE B:FDE201 0.3 64.1 0.5
NC B:FDE201 1.8 61.9 0.5
NA B:FDE201 2.0 34.5 0.5
ND B:FDE201 2.1 62.8 0.5
NC B:FDE201 2.1 32.6 0.5
NB B:FDE201 2.1 33.2 0.5
ND B:FDE201 2.1 35.4 0.5
NE2 B:HIS89 2.1 52.3 1.0
NB B:FDE201 2.2 62.5 0.5
NA B:FDE201 2.2 64.6 0.5
NE2 B:HIS55 2.3 33.2 1.0
C4C B:FDE201 2.9 60.8 0.5
C1C B:FDE201 2.9 60.7 0.5
CD2 B:HIS89 2.9 52.9 1.0
C1D B:FDE201 3.0 61.0 0.5
C1A B:FDE201 3.1 35.3 0.5
C4A B:FDE201 3.1 33.8 0.5
C4B B:FDE201 3.1 61.8 0.5
C4C B:FDE201 3.1 32.5 0.5
C1C B:FDE201 3.1 32.0 0.5
C4B B:FDE201 3.1 31.8 0.5
C1B B:FDE201 3.1 32.2 0.5
C1D B:FDE201 3.1 35.0 0.5
CE1 B:HIS55 3.1 33.1 1.0
C4D B:FDE201 3.2 35.9 0.5
C4D B:FDE201 3.2 62.1 0.5
C1B B:FDE201 3.3 63.1 0.5
C1A B:FDE201 3.3 64.4 0.5
CE1 B:HIS89 3.3 55.2 1.0
CHD B:FDE201 3.3 60.6 0.5
CD2 B:HIS55 3.3 33.9 1.0
C4A B:FDE201 3.3 64.5 0.5
CHC B:FDE201 3.4 61.5 0.5
CHD B:FDE201 3.5 33.7 0.5
CHB B:FDE201 3.5 32.6 0.5
CHA B:FDE201 3.5 36.3 0.5
CHC B:FDE201 3.5 32.6 0.5
CHA B:FDE201 3.6 63.9 0.5
CHB B:FDE201 3.7 64.0 0.5
C3C B:FDE201 4.1 59.4 0.5
C2C B:FDE201 4.1 61.1 0.5
CG B:HIS89 4.2 52.9 1.0
ND1 B:HIS55 4.3 31.9 1.0
ND1 B:HIS89 4.3 53.5 1.0
C2A B:FDE201 4.3 36.7 0.5
C3A B:FDE201 4.3 34.4 0.5
C2D B:FDE201 4.4 60.7 0.5
C2C B:FDE201 4.4 32.1 0.5
C3C B:FDE201 4.4 32.9 0.5
C2B B:FDE201 4.4 30.7 0.5
C3B B:FDE201 4.4 32.1 0.5
CG B:HIS55 4.4 32.3 1.0
C3B B:FDE201 4.4 62.4 0.5
C3D B:FDE201 4.5 61.9 0.5
C2D B:FDE201 4.5 36.6 0.5
C2B B:FDE201 4.5 63.7 0.5
C3D B:FDE201 4.5 37.0 0.5
C2A B:FDE201 4.6 64.8 0.5
C3A B:FDE201 4.6 65.8 0.5
CG2 B:VAL59 4.9 27.1 1.0

Reference:

A.H.Mcguire, A.R.Petit, J.Kang, T.Malewschik, V.De Serrano, L.M.Carey, R.A.Ghiladi. Nonnative Heme Incorporation Into Multifunctional Globin Increases Peroxygenase Activity An Order and Magnitude Compared to Native Enzyme To Be Published.
Page generated: Wed Aug 7 13:07:24 2024

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