Iron in PDB 6vd3: Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromophenol

Protein crystallography data

The structure of Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromophenol, PDB code: 6vd3 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) 33.77 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.656, 67.432, 67.547, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 18.8

Other elements in 6vd3:

The structure of Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromophenol 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) Mesoporphyrin IX and Substrate 4-Bromophenol (pdb code 6vd3). 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 Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromophenol, PDB code: 6vd3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6vd3

Go back to Iron Binding Sites List in 6vd3
Iron binding site 1 out of 2 in the Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromophenol


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) Mesoporphyrin IX and Substrate 4-Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:18.8
occ:1.00
FE A:MH0201 0.0 18.8 1.0
NB A:MH0201 2.0 19.3 1.0
NC A:MH0201 2.1 19.4 1.0
NA A:MH0201 2.1 19.3 1.0
ND A:MH0201 2.1 18.2 1.0
NE2 A:HIS89 2.2 22.4 1.0
C1B A:MH0201 3.1 19.1 1.0
C4A A:MH0201 3.1 19.1 1.0
C1D A:MH0201 3.1 19.1 1.0
C4C A:MH0201 3.1 18.8 1.0
C1C A:MH0201 3.1 19.4 1.0
C4B A:MH0201 3.1 20.5 1.0
C1A A:MH0201 3.1 18.9 1.0
C4D A:MH0201 3.1 18.9 1.0
CE1 A:HIS89 3.2 22.5 1.0
CD2 A:HIS89 3.2 22.0 1.0
CHB A:MH0201 3.4 19.3 1.0
CHD A:MH0201 3.4 19.7 1.0
CHC A:MH0201 3.4 20.4 1.0
CHA A:MH0201 3.5 17.8 1.0
C5 A:BML202 3.9 21.6 0.8
CG2 A:VAL59 4.3 14.9 1.0
C2B A:MH0201 4.3 20.6 1.0
C3A A:MH0201 4.3 18.3 1.0
C2D A:MH0201 4.3 19.2 1.0
C2C A:MH0201 4.3 19.6 1.0
C6 A:BML202 4.3 21.8 0.8
ND1 A:HIS89 4.3 21.6 1.0
C3B A:MH0201 4.3 21.0 1.0
C3C A:MH0201 4.3 19.6 1.0
C2A A:MH0201 4.3 19.7 1.0
C3D A:MH0201 4.3 19.9 1.0
CG A:HIS89 4.4 22.0 1.0
CG1 A:VAL59 4.6 14.6 1.0
CE A:MET86 4.9 24.1 1.0
C4 A:BML202 4.9 22.2 0.8

Iron binding site 2 out of 2 in 6vd3

Go back to Iron Binding Sites List in 6vd3
Iron binding site 2 out of 2 in the Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromophenol


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) Mesoporphyrin IX and Substrate 4-Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:22.1
occ:1.00
FE B:MH0201 0.0 22.1 1.0
NB B:MH0201 2.0 20.7 1.0
NC B:MH0201 2.0 22.2 1.0
NA B:MH0201 2.1 22.1 1.0
ND B:MH0201 2.1 21.0 1.0
NE2 B:HIS89 2.2 25.3 1.0
C1B B:MH0201 3.0 20.3 1.0
C1D B:MH0201 3.1 21.7 1.0
C4A B:MH0201 3.1 20.8 1.0
C4C B:MH0201 3.1 23.5 1.0
C4B B:MH0201 3.1 22.5 1.0
C1C B:MH0201 3.1 23.6 1.0
C1A B:MH0201 3.1 20.9 1.0
C4D B:MH0201 3.2 21.5 1.0
CE1 B:HIS89 3.2 24.7 1.0
CD2 B:HIS89 3.2 25.5 1.0
CHB B:MH0201 3.3 21.2 1.0
CHD B:MH0201 3.4 23.8 1.0
CHC B:MH0201 3.4 24.1 1.0
CHA B:MH0201 3.5 19.4 1.0
C5 B:BML202 3.8 22.1 0.8
C6 B:BML202 4.2 21.9 0.8
C2B B:MH0201 4.3 21.9 1.0
C2D B:MH0201 4.3 21.2 1.0
ND1 B:HIS89 4.3 23.6 1.0
C3B B:MH0201 4.3 22.8 1.0
C2C B:MH0201 4.3 24.0 1.0
C3A B:MH0201 4.3 21.3 1.0
C3C B:MH0201 4.3 24.5 1.0
CG B:HIS89 4.3 24.4 1.0
C3D B:MH0201 4.3 22.2 1.0
CG2 B:VAL59 4.4 16.1 1.0
C2A B:MH0201 4.4 22.2 1.0
C4 B:BML202 4.8 21.2 0.8

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: Sun Jan 24 17:03:02 2021

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