1D5L: Crystal Structure Of Cyanide-Bound Human Myeloperoxidase Isoform C At Ph 5.5

Citation:
Abstract
The 1.9 A X-ray crystal structure of human myeloperoxidase complexed with cyanide (R = 0.175, R(free) = 0.215) indicates that cyanide binds to the heme iron with a bent Fe-C-N angle of approximately 157 degrees, and binding is accompanied by movement of the iron atom by 0.2 A into the porphyrin plane. The bent orientation of the cyanide allows the formation of three hydrogen bonds between its nitrogen atom and the distal histidine as well as two water molecules in the distal cavity. The 1.85 A X-ray crystal structure of an inhibitory complex with thiocyanate (R = 0.178, R(free) = 0.210) indicates replacement of chloride at a proximal helix halide binding site in addition to binding in the distal cavity in an orientation parallel with the heme. The thiocyanate replaces two water molecules in the distal cavity and is hydrogen bonded to Gln 91. The 1.9 A structures of the complexes formed by bromide (R = 0.215, R(free) = 0.270) and thiocyanate (R = 0.198, R(free) = 0.224) with the cyanide complex of myeloperoxidase show how the presence of bound cyanide alters the binding site for bromide in the distal heme cavity, while having little effect on thiocyanate binding. These results support a model for a single common binding site for halides and thiocyanate as substrates or as inhibitors near the delta-meso carbon of the porphyrin ring in myeloperoxidase.
PDB ID: 1D5LDownload
MMDB ID: 48554
PDB Deposition Date: 1999/10/7
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 1.9  Å
Source Organism:
Similar Structures:
Biological Unit for 1D5L: tetrameric; determined by author and by software (PQS)
Molecular Components in 1D5L
Label Count Molecule
Proteins (4 molecules)
2
Myeloperoxidase(Gene symbol: MPO)
Molecule annotation
2
Myeloperoxidase(Gene symbol: MPO)
Molecule annotation
Chemicals (36 molecules)
1
2
2
3
3
4
4
2
5
8
6
2
7
4
8
2
9
2
10
7
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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