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Iron in PDB 1dnw: Human Myeloperoxidase-Cyanide-Thiocyanate Complex

Enzymatic activity of Human Myeloperoxidase-Cyanide-Thiocyanate Complex

All present enzymatic activity of Human Myeloperoxidase-Cyanide-Thiocyanate Complex:
1.11.1.7;

Protein crystallography data

The structure of Human Myeloperoxidase-Cyanide-Thiocyanate Complex, PDB code: 1dnw was solved by M.Blair-Johnson, T.J.Fiedler, R.E.Fenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.260, 63.770, 92.600, 90.00, 97.51, 90.00
R / Rfree (%) 19.7 / 22.4

Other elements in 1dnw:

The structure of Human Myeloperoxidase-Cyanide-Thiocyanate Complex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Human Myeloperoxidase-Cyanide-Thiocyanate Complex (pdb code 1dnw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Human Myeloperoxidase-Cyanide-Thiocyanate Complex, PDB code: 1dnw:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 1dnw

Go back to Iron Binding Sites List in 1dnw
Iron binding site 1 out of 2 in the Human Myeloperoxidase-Cyanide-Thiocyanate Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Myeloperoxidase-Cyanide-Thiocyanate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe14

b:13.0
occ:1.00
FE C:HEM14 0.0 13.0 1.0
NC C:HEM14 1.9 7.8 1.0
ND C:HEM14 2.0 9.8 1.0
NB C:HEM14 2.0 9.8 1.0
NA C:HEM14 2.0 9.6 1.0
NE2 C:HIS336 2.2 9.2 1.0
C A:CYN107 2.6 12.4 1.0
N A:CYN107 2.8 15.4 1.0
C4C C:HEM14 3.0 8.5 1.0
C1D C:HEM14 3.0 9.6 1.0
C1C C:HEM14 3.0 8.2 1.0
C4B C:HEM14 3.0 9.3 1.0
C1B C:HEM14 3.0 9.6 1.0
C4D C:HEM14 3.0 9.8 1.0
C1A C:HEM14 3.1 9.8 1.0
C4A C:HEM14 3.1 9.7 1.0
CD2 C:HIS336 3.2 8.9 1.0
CE1 C:HIS336 3.2 8.6 1.0
CHD C:HEM14 3.3 9.1 1.0
CHB C:HEM14 3.4 9.3 1.0
CHC C:HEM14 3.4 8.2 1.0
CHA C:HEM14 3.4 10.2 1.0
C3C C:HEM14 4.2 8.5 1.0
C2D C:HEM14 4.2 10.8 1.0
C2C C:HEM14 4.2 8.4 1.0
C3D C:HEM14 4.3 10.3 1.0
C3B C:HEM14 4.3 9.9 1.0
C2B C:HEM14 4.3 10.4 1.0
C2A C:HEM14 4.3 8.9 1.0
CG C:HIS336 4.3 8.5 1.0
C3A C:HEM14 4.3 9.2 1.0
ND1 C:HIS336 4.4 9.1 1.0
O C:HOH782 4.9 8.4 1.0
CD2 C:LEU417 4.9 8.6 1.0
NE2 A:GLN91 4.9 10.7 1.0

Iron binding site 2 out of 2 in 1dnw

Go back to Iron Binding Sites List in 1dnw
Iron binding site 2 out of 2 in the Human Myeloperoxidase-Cyanide-Thiocyanate Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Myeloperoxidase-Cyanide-Thiocyanate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe109

b:14.9
occ:1.00
FE B:HEM109 0.0 14.9 1.0
NB B:HEM109 2.0 12.5 1.0
NC B:HEM109 2.0 10.8 1.0
ND B:HEM109 2.0 10.4 1.0
NA B:HEM109 2.0 11.6 1.0
NE2 D:HIS336 2.2 12.1 1.0
C B:CYN108 2.3 18.8 1.0
N B:CYN108 2.9 19.0 1.0
C1B B:HEM109 3.0 13.7 1.0
C1C B:HEM109 3.0 11.4 1.0
C4B B:HEM109 3.0 13.2 1.0
C4D B:HEM109 3.0 9.5 1.0
C1D B:HEM109 3.0 9.8 1.0
C4C B:HEM109 3.0 10.2 1.0
C1A B:HEM109 3.1 11.4 1.0
C4A B:HEM109 3.1 12.1 1.0
CD2 D:HIS336 3.2 11.8 1.0
CE1 D:HIS336 3.2 10.8 1.0
CHC B:HEM109 3.4 11.5 1.0
CHB B:HEM109 3.4 13.5 1.0
CHA B:HEM109 3.4 11.5 1.0
CHD B:HEM109 3.4 9.2 1.0
C2B B:HEM109 4.2 14.3 1.0
C2C B:HEM109 4.3 10.6 1.0
C3C B:HEM109 4.3 10.8 1.0
C3B B:HEM109 4.3 13.3 1.0
C3D B:HEM109 4.3 9.4 1.0
C2D B:HEM109 4.3 8.3 1.0
C2A B:HEM109 4.3 10.6 1.0
C3A B:HEM109 4.3 10.7 1.0
CG D:HIS336 4.3 11.0 1.0
ND1 D:HIS336 4.3 11.5 1.0
O D:HOH797 4.8 8.7 1.0
NE2 B:GLN91 4.8 6.6 1.0
CD2 D:LEU417 4.9 6.6 1.0

Reference:

M.Blair-Johnson, T.Fiedler, R.Fenna. Human Myeloperoxidase: Structure of A Cyanide Complex and Its Interaction with Bromide and Thiocyanate Substrates at 1.9 A Resolution. Biochemistry V. 40 13990 2001.
ISSN: ISSN 0006-2960
PubMed: 11705390
DOI: 10.1021/BI0111808
Page generated: Sun Dec 13 14:10:49 2020

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