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

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

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

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 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 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 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

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.