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Iron in PDB 1d2v: Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5

Enzymatic activity of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5

All present enzymatic activity of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5, PDB code: 1d2v was solved by T.J.Fiedler, C.A.Davey, R.E.Fenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.155, 63.488, 92.476, 90.00, 97.36, 90.00
R / Rfree (%) 24.3 / 29.6

Other elements in 1d2v:

The structure of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 also contains other interesting chemical elements:

Bromine (Br) 8 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 (pdb code 1d2v). 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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5, PDB code: 1d2v:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 1d2v

Go back to Iron Binding Sites List in 1d2v
Iron binding site 1 out of 2 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe605

b:6.4
occ:1.00
FE A:HEM605 0.0 6.4 1.0
NC A:HEM605 2.0 7.9 1.0
NA A:HEM605 2.0 6.6 1.0
ND A:HEM605 2.0 4.8 1.0
NB A:HEM605 2.0 6.5 1.0
NE2 C:HIS336 2.2 4.6 1.0
O A:HOH844A 2.8 8.6 1.0
C4C A:HEM605 3.0 8.3 1.0
C1A A:HEM605 3.0 6.7 1.0
C1C A:HEM605 3.0 4.4 1.0
C1D A:HEM605 3.0 6.8 1.0
C4D A:HEM605 3.0 3.1 1.0
C4A A:HEM605 3.0 5.7 1.0
C4B A:HEM605 3.1 5.3 1.0
C1B A:HEM605 3.1 5.2 1.0
CD2 C:HIS336 3.1 2.0 1.0
CE1 C:HIS336 3.1 2.0 1.0
CHD A:HEM605 3.4 8.8 1.0
CHA A:HEM605 3.4 5.7 1.0
CHC A:HEM605 3.4 4.8 1.0
CHB A:HEM605 3.4 3.9 1.0
CG C:HIS336 4.2 2.0 1.0
C3C A:HEM605 4.2 6.7 1.0
C2A A:HEM605 4.3 5.4 1.0
C2C A:HEM605 4.3 5.8 1.0
C3A A:HEM605 4.3 4.7 1.0
C2D A:HEM605 4.3 7.6 1.0
C3D A:HEM605 4.3 5.0 1.0
ND1 C:HIS336 4.3 4.2 1.0
C2B A:HEM605 4.3 4.6 1.0
C3B A:HEM605 4.3 4.3 1.0
CD2 C:LEU417 4.7 3.0 1.0

Iron binding site 2 out of 2 in 1d2v

Go back to Iron Binding Sites List in 1d2v
Iron binding site 2 out of 2 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe605

b:9.3
occ:1.00
FE B:HEM605 0.0 9.3 1.0
NC B:HEM605 2.0 4.5 1.0
NB B:HEM605 2.0 5.5 1.0
NA B:HEM605 2.0 8.4 1.0
ND B:HEM605 2.0 6.3 1.0
NE2 D:HIS336 2.2 9.1 1.0
O B:HOH844B 3.0 21.1 1.0
C4C B:HEM605 3.0 4.4 1.0
C1C B:HEM605 3.0 2.0 1.0
C1D B:HEM605 3.0 5.8 1.0
C1B B:HEM605 3.0 3.8 1.0
C4A B:HEM605 3.0 8.5 1.0
C4B B:HEM605 3.0 4.2 1.0
C1A B:HEM605 3.1 7.5 1.0
C4D B:HEM605 3.1 6.1 1.0
CD2 D:HIS336 3.1 6.0 1.0
CE1 D:HIS336 3.2 5.8 1.0
CHD B:HEM605 3.4 5.1 1.0
CHB B:HEM605 3.4 5.8 1.0
CHC B:HEM605 3.4 2.0 1.0
CHA B:HEM605 3.5 5.2 1.0
C2C B:HEM605 4.2 3.3 1.0
C3C B:HEM605 4.3 5.9 1.0
CG D:HIS336 4.3 6.2 1.0
C2B B:HEM605 4.3 2.9 1.0
C3A B:HEM605 4.3 6.6 1.0
C2A B:HEM605 4.3 7.4 1.0
C2D B:HEM605 4.3 6.1 1.0
C3B B:HEM605 4.3 3.7 1.0
C3D B:HEM605 4.3 6.1 1.0
ND1 D:HIS336 4.3 6.4 1.0
CD2 D:LEU417 4.6 5.7 1.0
NE2 B:GLN91 5.0 3.2 1.0
BR B:BR843 5.0 12.6 0.4

Reference:

T.J.Fiedler, C.A.Davey, R.E.Fenna. X-Ray Crystal Structure and Characterization of Halide-Binding Sites of Human Myeloperoxidase at 1.8 A Resolution. J.Biol.Chem. V. 275 11964 2000.
ISSN: ISSN 0021-9258
PubMed: 10766826
DOI: 10.1074/JBC.275.16.11964
Page generated: Sun Dec 13 14:10:04 2020

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